sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001404275,"{'34': 92.9, '33F2': 34.7, '35B': 30.7, '33F': 29.0, '33C': 28.0}",1,92.9,,34,,,{},{},34,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170915,"{'23B': 99.3, '23B1': 64.6, '23F': 45.8, '23A': 40.0, '06A-IV': 36.6}",1,99.3,,23B,,,{},{},23B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001346435,"{'10A': 99.4, '10B': 67.1, '10C': 27.7, '10F': 18.1, '22F': 15.4}",1,99.4,,10A,,,{},{},10A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001345435,"{1: 0.6, 20: 0.3, 14: 0.2}",1,0.6,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001160725,"{'06E': 100.0, '06B-III': 97.4, '06B-I': 44.7, '06A-III': 44.2, '06B-II': 43.6}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001159025,"{'19A': 99.8, '19A-III': 99.6, '19A-I': 86.0, '19A-II': 83.5, '19AF': 57.2}",1,99.8,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(100.0)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_019446375,"{'20': 98.9, '13': 26.1, '09L': 25.0, '36': 24.9, '47F': 24.1}",1,98.9,,20,,,{},{},20,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001118005,"{'38': 88.6, '25F': 84.8, '25A': 83.9, '36': 10.9, '20': 6.5}",1,88.6,25F_25A_38,25F_25A_38,,"[[0], [18]]","{'wcyD': ['b: 22.59'], 'wcyV': np.float64(4.69)}","{'wcyD': 0, 'wcyV': 'not_detected'}",25F_25A_38,RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007787205,"{'01': 6.7, '45': 5.9, '25F': 5.7, '20': 5.5, '25A': 5.5}",3,6.7,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001581155,"{'01': 26.3, '06C': 20.4, '06C-I': 20.4, '06A-V': 19.7, '06A-II': 19.6}",1,26.3,,"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",,,{},{},"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_002889635,"{'07C': 0.2, '17F': 0.2, '07B': 0.1, '40': 0.1}",1,0.2,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001151885,"{'11F': 61.1, '11D': 38.4, '11A': 36.8, '09V': 24.5, '09A': 24.4}",1,61.1,,"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",,,{},{},"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900191305,"{'01': 93.9, '19F': 32.3, '19F-I': 31.8, '19F-III': 31.6, '19F-II': 31.3}",1,93.9,,1,,,{},{},1,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907167495,"{'14': 91.3, '36': 26.5, '09L': 24.6, '09N': 23.9, '15B': 23.4}",1,91.3,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001329235,"{'06E': 100.0, '06B-III': 96.2, '06B-I': 43.6, '06A-III': 43.1, '06A-I': 42.6}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001120305,"{'15C': 87.7, '15B': 87.6, '15A': 64.5, '15F': 49.9, '23A': 30.2}",1,87.7,,15B/15C,,,{},{},15B/15C,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907170015,"{'14': 92.1, '23F': 79.8, '23A': 63.7, '06A-IV': 45.6, '06B-II': 43.8}",1,92.1,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007785115,"{'03': 75.1, '01': 7.0, '06A-IV': 6.5, '20': 6.4, '36': 6.2}",1,75.1,,3,,,{},{},3,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_020038005,"{'16F': 96.8, '18F': 46.1, '19F-II': 45.5, '18B': 45.3, '18C': 45.2}",1,96.8,,16F,,,{},{},16F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907169065,"{'14': 90.9, '36': 25.8, '09L': 24.9, '09N': 23.8, '15B': 23.3}",1,90.9,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900044825,"{'07A': 99.6, '07F': 99.4, '22F': 69.2, '22A': 51.0, '16A': 39.4}",1,99.6,,7F/7A,,,{},{},7F/7A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907168795,"{'14': 91.4, '36': 26.2, '09L': 24.3, '15B': 23.4, '15C': 23.3}",1,91.4,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001120425,"{'23F': 94.0, '23A': 63.5, '28A': 48.5, '23B': 47.0, '06A-III': 46.3}",1,94.0,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001134745,"{'07A': 89.1, '07F': 88.9, '19F-II': 38.3, '19F': 37.0, '19F-IV': 36.8}",1,89.1,,7F/7A,,,{},{},7F/7A,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001191995,"{'06E': 99.8, '06B-III': 97.8, '06B-I': 45.3, '06A-III': 44.8, '06B-II': 44.0}",1,99.8,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001098585,"{'19F-I': 95.5, '19F': 95.2, '19F-III': 93.7, '19F-II': 92.4, '19F-IV': 88.4}",1,95.5,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001155585,"{'19F-I': 95.7, '19F': 95.4, '19F-III': 93.9, '19F-II': 92.6, '19F-IV': 88.6}",1,95.7,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001089145,"{'38': 88.2, '25F': 84.4, '25A': 83.6, '36': 11.8, '20': 7.7}",1,88.2,25F_25A_38,25F_25A_38,,"[[0], [18]]","{'wcyD': ['b: 22.59'], 'wcyV': np.float64(4.69)}","{'wcyD': 0, 'wcyV': 'not_detected'}",25F_25A_38,RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170425,"{'14': 92.0, '36': 28.4, '09L': 25.3, '09N': 24.2, '15B': 23.9}",1,92.0,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001088685,"{'06A': 90.4, '06A-III': 89.4, '06A-II': 89.3, '06A-VI': 89.3, '06B-II': 89.3}",1,90.4,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(93.22)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907168785,"{'19A': 100.0, '19A-III': 99.8, '19A-I': 86.2, '19A-II': 83.7, '19AF': 57.2}",1,100.0,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(100.0)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_012911325,"{'35B': 69.7, '33F': 33.3, '34': 33.3, '35C': 33.2, '35A': 32.8}",1,69.7,,"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",,,{},{},"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001140945,"{'19F-I': 77.0, '19F': 76.6, '19F-III': 75.6, '19F-II': 73.5, '19F-IV': 69.4}",1,77.0,,19F,,,{},{},19F,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_923172325,"{'22F': 1.2, '01': 0.7, '36': 0.7, '06A-IV': 0.7, '06C': 0.3}",1,1.2,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907168645,"{'19A': 100.0, '19A-III': 99.8, '19A-I': 86.2, '19A-II': 83.7, '19AF': 57.2}",1,100.0,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(100.0)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001342715,"{'22F': 85.8, '22A': 71.4, '06A': 39.6, '06A-III': 39.5, '06A-I': 39.4}",1,85.8,,22F,,,{},{},22F,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001581215,"{'08': 99.8, '06A-II': 24.7, '06A-VI': 24.6, '02': 24.4, '06B-II': 24.1}",1,99.8,,8,,,{},{},8,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171135,"{'19F-III': 98.4, '19F': 98.0, '19F-I': 98.0, '19F-II': 93.8, '19F-IV': 89.2}",1,98.4,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007784945,"{'45': 6.5, '01': 6.2, '25F': 5.8, '25A': 5.6, '22F': 5.0}",2,6.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001173765,"{'19F-I': 92.8, '19F': 92.5, '19F-III': 91.0, '19F-II': 90.2, '19F-IV': 86.2}",1,92.8,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001122945,"{'06E': 99.8, '06B-III': 97.1, '06B-I': 45.5, '06A-III': 45.0, '06A-II': 44.1}",1,99.8,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001209285,"{'21': 92.0, '22F': 34.4, '06A-IV': 34.2, '06A-II': 33.9, '06A-VI': 33.9}",1,92.0,,21,,,{},{},21,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170115,"{'06E': 100.0, '06B-III': 99.5, '06B-I': 46.9, '06A-III': 46.4, '06A-II': 45.4}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001581135,"{'45': 6.5, '25F': 5.8, '25A': 5.6, '01': 5.4, '22F': 5.2}",3,6.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170865,"{'06C-I': 99.9, '06C': 99.7, '06D': 84.6, '06A-II': 79.5, '06A-VI': 79.5}",1,99.9,6A_6B_6C_6D,6A_6B_6C_6D,,[[2]],"{'wciN': ['b', np.float64(91.3)]}",{'wciN': 'b'},6C/6D,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170715,"{'16F': 96.7, '19F-IV': 44.8, '19F-II': 44.0, '19F': 43.0, '19F-I': 42.4}",1,96.7,,16F,,,{},{},16F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_018253915,"{'24F2': 99.7, '24B': 88.5, '24F': 87.0, '24A': 71.0, '07B': 56.8}",1,99.7,,24F/24B,,,{},{},24F/24B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001108185,"{'19F': 95.6, '19F-I': 95.6, '19F-III': 94.0, '19F-II': 92.5, '19F-IV': 88.5}",1,95.6,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001096225,"{'33C': 98.7, '34': 29.9, '35B': 24.9, '33F2': 23.8, '33F': 23.0}",1,98.7,,33C,,,{},{},33C,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000762765,"{'20': 5.2, '01': 5.0, '22F': 3.8, '45': 3.6, '06C-I': 3.3}",1,5.2,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001581275,"{'06A-II': 94.7, '06A-VI': 94.7, '06B-II': 88.8, '06A-V': 88.3, '06A-III': 87.8}",1,94.7,6A_6B_6C_6D,6A_6B_6C_6D,,[[0]],{'wciN': ['a: 89.29']},{'wciN': 0},6A_6B_6C_6D,RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001138125,"{'15C': 87.7, '15B': 87.6, '15A': 64.5, '15F': 49.9, '23A': 30.2}",1,87.7,,15B/15C,,,{},{},15B/15C,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001194745,"{'23F': 94.5, '23A': 63.5, '06A-IV': 53.2, '06B-II': 51.6, '23B': 50.8}",1,94.5,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001135965,"{'19A': 99.3, '19A-III': 99.1, '19A-I': 86.2, '19A-II': 83.9, '19AF': 57.2}",1,99.3,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(100.0)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_009720645,"{'19A-I': 97.0, '19A-II': 95.1, '19A': 90.2, '19A-III': 90.0, '19AF': 61.3}",1,97.0,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(94.25)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001211125,"{'06A-III': 82.1, '06B-I': 81.2, '06A-II': 78.0, '06A-VI': 78.0, '06B-II': 76.1}",1,82.1,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(96.5)]}",{'wciN': 'a'},6A/6B,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001131245,"{'06E': 99.9, '06B-III': 99.3, '06B-I': 46.6, '06A-III': 46.1, '06A-II': 45.1}",1,99.9,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907170665,"{'14': 92.6, '36': 27.8, '09L': 25.2, '09N': 24.3, '15B': 24.2}",1,92.6,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001115385,"{'36': 10.1, '23B1': 6.8, '45': 6.1, '06A-IV': 6.1, '01': 5.9}",1,10.1,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_003933525,"{'23B': 82.5, '23B1': 56.8, '23F': 38.6, '06A-IV': 33.9, '23A': 33.2}",1,82.5,,23B,,,{},{},23B,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001163525,"{'23F': 94.0, '23A': 63.5, '28A': 48.5, '23B': 47.0, '06A-III': 46.4}",1,94.0,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001199155,"{'23F': 94.0, '23A': 63.5, '28A': 48.5, '23B': 47.0, '06A-III': 46.4}",1,94.0,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170195,"{'06C-I': 99.4, '06C': 99.2, '06D': 84.6, '06A-II': 79.0, '06A-VI': 79.0}",1,99.4,6A_6B_6C_6D,6A_6B_6C_6D,,[[2]],"{'wciN': ['b', np.float64(91.3)]}",{'wciN': 'b'},6C/6D,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901277915,"{'06E': 96.8, '06B-III': 96.6, '06B-I': 46.6, '06A-III': 46.1, '06A-II': 45.3}",1,96.8,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170065,"{'06E': 100.0, '06B-III': 99.3, '06B-I': 46.8, '06A-III': 46.3, '06A-II': 45.3}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_010604195,"{'19A': 99.3, '19A-III': 99.1, '19A-I': 86.2, '19A-II': 83.9, '19AF': 57.2}",1,99.3,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(100.0)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001160105,"{'19A-I': 99.4, '19A-II': 97.7, '19A': 88.0, '19A-III': 87.8, '19AF': 62.0}",1,99.4,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(95.25)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907167835,"{'09A': 98.9, '09V': 98.7, '09N': 36.7, '09L': 35.2, '11F': 26.6}",1,98.9,,9A/9V,,,{},{},9A/9V,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001174105,"{'34': 92.9, '33F2': 34.7, '35B': 30.4, '33F': 29.0, '33C': 28.0}",1,92.9,,34,,,{},{},34,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901218265,"{'03': 97.4, '20': 16.6, '01': 15.9, '36': 15.6, '09L': 14.7}",1,97.4,,3,,,{},{},3,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001719955,"{'19F-I': 98.0, '19F': 97.3, '19F-III': 96.8, '19F-II': 95.3, '19F-IV': 90.4}",1,98.0,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171385,"{'19F-II': 99.5, '19F': 95.3, '19F-III': 94.3, '19F-I': 94.0, '19F-IV': 93.2}",1,99.5,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907170115,"{'14': 92.7, '36': 28.8, '09L': 25.8, '15B': 25.5, '09N': 25.3}",1,92.7,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_002021715,"{'01': 7.0, '36': 7.0, '45': 6.9, '20': 5.9, '22F': 5.3}",3,7.0,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901248835,"{'19A-I': 99.4, '19A-II': 97.7, '19A': 88.0, '19A-III': 87.8, '19AF': 62.0}",1,99.4,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(95.25)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001120105,"{'01': 5.5, '25F': 4.9, '25A': 4.7, '38': 3.7, '35B': 3.4}",1,5.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001169085,"{'22A': 94.2, '22F': 76.3, '06A-IV': 45.8, '06A-II': 44.1, '06B-I': 44.1}",1,94.2,,22A,,,{},{},22A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170695,"{'06E': 99.9, '06B-III': 99.5, '06B-I': 46.9, '06A-III': 46.4, '06A-II': 45.4}",1,99.9,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001545505,"{'06E': 99.9, '06B-III': 99.3, '06B-I': 46.9, '06A-III': 46.4, '06A-II': 45.4}",1,99.9,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007787115,"{'03': 97.4, '01': 17.2, '09N': 15.4, '20': 15.3, '09L': 15.1}",1,97.4,,3,,,{},{},3,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907170165,"{'14': 91.8, '36': 26.7, '09L': 23.9, '15B': 23.7, '15C': 23.6}",1,91.8,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_012911195,"{'35B': 58.7, '33F': 32.4, '34': 31.9, '35C': 31.7, '35A': 31.3}",1,58.7,,"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",,,{},{},"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900172415,"{'19A-I': 99.7, '19A-II': 97.5, '19A': 87.7, '19A-III': 87.5, '19AF': 61.8}",1,99.7,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(95.25)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170285,"{'06C-I': 99.6, '06C': 99.4, '06D': 84.6, '06A-II': 79.2, '06A-VI': 79.2}",1,99.6,6A_6B_6C_6D,6A_6B_6C_6D,,[[2]],"{'wciN': ['b', np.float64(91.3)]}",{'wciN': 'b'},6C/6D,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001348095,"{'14': 94.6, '36': 24.7, '15B': 24.2, '15C': 24.1, '09L': 23.1}",1,94.6,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001117705,"{'19A-I': 99.3, '19A-II': 98.3, '19A': 90.2, '19A-III': 90.0, '06A': 74.9}",1,99.3,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(95.25)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001300155,"{'06A': 100.0, '06A-IV': 99.6, '06B-II': 95.4, '06A-V': 93.7, '06A-III': 91.7}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(100.0)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001089105,"{'19A': 100.0, '19A-III': 99.8, '19A-I': 86.2, '19A-II': 83.7, '19AF': 57.2}",1,100.0,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(100.0)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001117805,"{'25F': 5.3, '25A': 5.1, '22F': 4.9, '01': 4.6, '38': 4.2}",1,5.3,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001205615,"{'15C': 87.9, '15B': 87.7, '15A': 64.6, '15F': 50.0, '23A': 30.2}",1,87.9,,15B/15C,,,{},{},15B/15C,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901248505,"{'12F': 95.7, '12B': 93.1, '44': 92.7, '12A': 84.3, '46': 81.2}",1,95.7,12F_12A_12B_44_46,12F_12A_12B_44_46,,[[5]],"{'wciI': [2, np.float64(94.56)]}",{'wciI': 2},12F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171665,"{'06D': 87.2, '06C': 85.2, '06C-I': 85.2, '06A-I': 76.0, '06B': 75.9}",1,87.2,6A_6B_6C_6D,6A_6B_6C_6D,,[[0]],{'wciN': ['b: 89.8']},{'wciN': 0},6A_6B_6C_6D,RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001097905,"{'25F': 5.8, '25A': 5.6, '22F': 4.9, '38': 4.8, '12A': 4.6}",2,5.8,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001090745,"{'01': 7.2, '45': 6.2, '20': 5.6, '25F': 5.6, '25A': 5.4}",2,7.2,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170445,"{'14': 92.6, '36': 28.9, '09L': 25.4, '09N': 24.2, '15B': 24.2}",1,92.6,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001146085,"{'01': 2.9, '22F': 0.7, '38': 0.5, '25A': 0.4, '25F': 0.4}",1,2.9,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001102125,"{'03': 95.2, '36': 16.9, '20': 15.2, '14': 13.6, '09L': 13.3}",1,95.2,,3,,,{},{},3,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001107245,"{'33B': 89.8, '33D': 89.7, '35B': 32.9, '33F2': 30.0, '22F': 27.3}",1,89.8,,"Mixed serotypes- {'33D', '33B'}",,,{},{},"Mixed serotypes- {'33D', '33B'}",AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001343975,"{'23F': 94.5, '23A': 63.5, '06A-IV': 53.2, '06B-II': 51.6, '23B': 50.8}",1,94.5,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001143925,"{'06E': 100.0, '06B-III': 95.4, '06B-I': 42.7, '06A-I': 42.6, '06B': 42.2}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001124325,"{'38': 87.8, '25F': 84.0, '25A': 83.2, '36': 11.4, '20': 7.4}",1,87.8,25F_25A_38,25F_25A_38,,"[[0], [18]]","{'wcyD': ['b: 22.59'], 'wcyV': np.float64(4.69)}","{'wcyD': 0, 'wcyV': 'not_detected'}",25F_25A_38,RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001330795,"{'19F-I': 95.7, '19F': 95.4, '19F-III': 93.8, '19F-II': 92.6, '19F-IV': 88.6}",1,95.7,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000355985,"{'01': 91.4, '19F': 32.0, '19F-I': 31.5, '19F-III': 31.3, '19F-II': 31.0}",1,91.4,,1,,,{},{},1,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001165205,"{'37': 98.8, '33F': 77.0, '33A': 75.7, '33F2': 70.4, '35B': 31.2}",1,98.8,,37,,,{},{},37,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007787395,"{'45': 6.5, '25F': 5.8, '25A': 5.6, '22F': 5.5, '38': 4.9}",3,6.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007785135,"{'13': 95.4, '09N': 29.1, '20': 28.9, '09L': 28.7, '36': 28.0}",1,95.4,,13,,,{},{},13,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001126825,"{'34': 92.8, '33F2': 34.7, '35B': 30.2, '33F': 29.0, '33C': 28.1}",1,92.8,,34,,,{},{},34,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001120025,"{'15C': 95.2, '15B': 95.1, '15A': 60.9, '15F': 47.3, '23A': 34.5}",1,95.2,,15B/15C,,,{},{},15B/15C,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_002889795,"{'23F': 93.2, '23A': 62.4, '06A-IV': 53.1, '06B-II': 51.5, '06A-V': 50.7}",1,93.2,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001330435,"{'19F-I': 95.7, '19F': 95.4, '19F-III': 93.9, '19F-II': 92.6, '19F-IV': 88.6}",1,95.7,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001585515,"{'12F': 93.8, '44': 90.7, '12B': 90.6, '12A': 82.9, '46': 79.8}",1,93.8,12F_12A_12B_44_46,12F_12A_12B_44_46,,[[5]],"{'wciI': [2, np.float64(94.56)]}",{'wciI': 2},12F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170795,"{'01': 6.9, '25F': 5.7, '25A': 5.5, '20': 5.4, '45': 5.4}",2,6.9,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907168525,"{'19A': 99.8, '19A-III': 99.6, '19A-I': 86.0, '19A-II': 83.5, '19AF': 57.2}",1,99.8,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(100.0)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001143365,"{'15C': 87.7, '15B': 87.6, '15A': 64.5, '15F': 49.9, '23A': 30.2}",1,87.7,,15B/15C,,,{},{},15B/15C,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001128405,"{'19F-I': 95.8, '19F': 95.5, '19F-III': 93.9, '19F-II': 92.8, '19F-IV': 88.7}",1,95.8,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_012911115,"{'35B': 84.4, '34': 33.3, '33F': 33.0, '35C': 32.8, '35A': 32.4}",1,84.4,,35B/35D,,,{},{},35B/35D,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171315,"{'19F-II': 99.6, '19F': 95.4, '19F-III': 94.4, '19F-I': 94.1, '19F-IV': 93.3}",1,99.6,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907168535,"{'19A': 100.0, '19A-III': 99.8, '19A-I': 86.2, '19A-II': 83.7, '19AF': 57.2}",1,100.0,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(100.0)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901245585,"{'06B-III': 89.4, '06E': 88.8, '06B-I': 50.0, '06A-III': 49.5, '06A-II': 48.8}",1,89.4,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001103405,"{'19F': 89.4, '19F-I': 89.2, '19F-III': 87.6, '19F-II': 86.9, '19F-IV': 82.7}",1,89.4,,19F,,,{},{},19F,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000385735,"{'06A-III': 89.2, '06B-I': 88.6, '06A-II': 87.7, '06A-VI': 87.7, '06A-V': 87.5}",1,89.2,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(96.5)]}",{'wciN': 'a'},6A/6B,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907167565,"{'14': 88.6, '36': 24.5, '09L': 23.9, '09N': 22.9, '15B': 21.3}",1,88.6,,14,,,{},{},14,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171645,"{'19F-III': 98.4, '19F': 98.0, '19F-I': 98.0, '19F-II': 93.8, '19F-IV': 89.2}",1,98.4,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_009721075,"{'23A': 48.1, '23F': 47.2, '28A': 38.4, '28F': 37.5, '01': 34.0}",1,48.1,,"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",,,{},{},"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000179855,"{'19A': 32.0, '19A-III': 32.0, '19A-I': 28.9, '19A-II': 28.1, '19AF': 18.9}",1,32.0,,"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",,,{},{},"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001131565,"{'19F-I': 95.7, '19F': 95.4, '19F-III': 93.9, '19F-II': 92.6, '19F-IV': 88.6}",1,95.7,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001086305,"{'36': 6.5, '06A-IV': 4.6, '12A': 4.5, '46': 4.5, '20': 3.7}",1,6.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001156345,"{'19F-I': 95.7, '19F': 95.4, '19F-III': 93.9, '19F-II': 92.6, '19F-IV': 88.6}",1,95.7,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001078685,"{'36': 11.1, '06A-IV': 7.7, '20': 7.0, '06C': 6.4, '06B-I': 6.4}",1,11.1,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001090185,"{'10A': 94.0, '10B': 64.6, '10C': 29.3, '10F': 19.7, '47A': 16.8}",1,94.0,,10A,,,{},{},10A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901215125,"{'19A': 92.6, '19A-III': 92.4, '19A-II': 83.3, '19A-I': 81.3, '19AF': 56.1}",1,92.6,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(97.62)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001719745,"{'06E': 97.7, '06B-III': 97.4, '06B-I': 46.5, '06A-III': 46.0, '06A-II': 45.4}",1,97.7,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001339675,"{'19F-I': 95.7, '19F': 95.4, '19F-III': 93.9, '19F-II': 92.6, '19F-IV': 88.6}",1,95.7,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001095265,"{'06E': 100.0, '06B-III': 97.6, '06B-I': 44.9, '06A-III': 44.4, '06B-II': 43.8}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901245195,"{'36': 12.0, '01': 7.5, '20': 7.3, '06A-IV': 7.2, '45': 6.7}",1,12.0,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000411775,"{'45': 6.5, '25F': 6.2, '25A': 6.0, '01': 5.8, '38': 4.8}",2,6.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001107185,"{'06E': 100.0, '06B-III': 95.2, '06A-I': 42.6, '06B-I': 42.5, '06B': 42.2}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001133605,"{'23F': 70.3, '23A': 54.5, '19F-I': 43.0, '19F': 42.6, '19F-II': 42.5}",1,70.3,,23F,,,{},{},23F,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171445,"{'23A': 99.7, '23F': 67.3, '23B': 43.6, '19F-II': 37.9, '15B': 37.2}",1,99.7,,23A,,,{},{},23A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001343315,"{'06E': 100.0, '06B-III': 98.6, '06B-I': 46.2, '06A-III': 45.7, '06A-II': 44.7}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001161965,"{'06B-III': 87.4, '06E': 86.7, '06B-I': 51.0, '06A-III': 50.6, '06C': 50.5}",1,87.4,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001203215,"{'19F-I': 95.7, '19F': 95.4, '19F-III': 93.9, '19F-II': 92.6, '19F-IV': 88.6}",1,95.7,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170375,"{'23F': 92.6, '23A': 61.3, '28A': 48.1, '23B': 46.8, '06A-IV': 46.6}",1,92.6,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_018335455,"{'23B1': 99.8, '23B': 55.5, '19A-II': 36.2, '19A-I': 35.9, '19AF': 31.1}",1,99.8,,23B,,,{},{},23B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001095025,"{'19F-I': 95.7, '19F': 95.4, '19F-III': 93.9, '19F-II': 92.6, '19F-IV': 88.6}",1,95.7,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170265,"{'05': 95.3, '45': 22.1, '36': 21.5, '20': 20.1, '12A': 19.8}",1,95.3,,5,,,{},{},5,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907170295,"{'14': 88.0, '36': 26.2, '09L': 23.1, '09N': 22.4, '15B': 21.9}",1,88.0,,14,,,{},{},14,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001329415,"{'19A': 99.4, '19A-III': 99.2, '19A-I': 86.1, '19A-II': 83.9, '19AF': 57.2}",1,99.4,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(100.0)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001121665,"{'06A-II': 97.9, '06A-VI': 97.9, '06B-II': 90.4, '06A-V': 89.6, '06A-III': 89.2}",1,97.9,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(93.22)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001197315,"{'23F': 94.0, '23A': 63.5, '28A': 48.5, '23B': 47.0, '06A-III': 46.4}",1,94.0,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_012911415,"{'35B': 87.8, '33F': 33.1, '34': 33.1, '35C': 33.0, '35A': 32.6}",1,87.8,,35B/35D,,,{},{},35B/35D,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_009720945,"{'15C': 95.7, '15B': 95.6, '15A': 66.8, '15F': 56.2, '11D': 53.2}",1,95.7,,15B/15C,,,{},{},15B/15C,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170965,"{'23B': 99.4, '23B1': 64.6, '23F': 45.6, '23A': 39.8, '06A-IV': 36.6}",1,99.4,,23B,,,{},{},23B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_002889915,"{'35A': 99.6, '35C': 84.9, '42': 84.3, '33A': 42.9, '33F': 42.6}",1,99.6,,35A/35C/42,,,{},{},35A/35C/42,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901234155,"{'14': 99.7, '36': 29.8, '09L': 27.2, '09N': 25.0, '15B': 24.3}",1,99.7,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171055,"{'33F': 100.0, '33A': 97.5, '33F2': 70.9, '35C': 42.8, '42': 41.8}",1,100.0,,33F/33A,,,{},{},33F/33A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901235425,"{'06B-I': 97.0, '06A-III': 94.7, '06B-II': 88.4, '06A': 87.9, '06A-V': 86.5}",1,97.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(100.0)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_002866085,"{'01': 6.5, '45': 6.2, '20': 5.7, '25F': 5.7, '25A': 5.5}",2,6.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_003933625,"{'35B': 92.6, '33F': 33.4, '34': 33.3, '35C': 33.2, '35A': 32.8}",1,92.6,,35B/35D,,,{},{},35B/35D,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170685,"{'10A': 100.0, '10B': 66.8, '10C': 27.5, '10F': 17.9, '22F': 14.4}",1,100.0,,10A,,,{},{},10A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900050145,"{'05': 95.2, '09L': 94.4, '09N': 84.9, '36': 34.2, '09A': 31.9}",1,95.2,,"Mixed serotypes- {'5', '9N/9L'}",,,{},{},"Mixed serotypes- {'5', '9N/9L'}",AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901254525,"{'23A': 96.0, '23F': 68.8, '23B': 40.1, '19F-II': 37.8, '15B': 37.4}",1,96.0,,23A,,,{},{},23A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001152285,"{'10B': 99.4, '10A': 65.2, '10F': 20.1, '10C': 18.8, '22F': 14.0}",1,99.4,,10B,,,{},{},10B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007784665,"{'01': 7.4, '45': 6.3, '25F': 5.7, '25A': 5.5, '22F': 5.2}",4,7.4,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001581745,"{'24F': 90.9, '24B': 83.8, '24F2': 80.5, '24A': 62.9, '07C': 46.1}",1,90.9,,24F/24B,,,{},{},24F/24B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007786755,"{'01': 6.8, '45': 5.8, '25F': 5.7, '20': 5.5, '25A': 5.5}",3,6.8,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007786955,"{'01': 7.2, '45': 6.4, '25F': 5.4, '25A': 5.2, '22F': 5.1}",4,7.2,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001151965,"{'19F-I': 95.7, '19F': 95.4, '19F-III': 93.9, '19F-II': 92.6, '19F-IV': 88.6}",1,95.7,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001207275,"{'14': 94.5, '15B': 24.2, '15C': 24.1, '09L': 23.0, '19F-II': 22.4}",1,94.5,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007785095,"{'01': 6.7, '45': 6.4, '25F': 5.8, '25A': 5.6, '22F': 5.3}",3,6.7,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001198475,"{'06E': 99.9, '06B-III': 98.3, '06B-I': 45.9, '06A-III': 45.4, '06A-II': 44.4}",1,99.9,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001115005,"{'06E': 100.0, '06B-III': 94.4, '06A-I': 42.6, '06B': 42.2, '06B-I': 41.8}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001581775,"{'01': 7.1, '45': 5.8, '25F': 5.7, '20': 5.5, '25A': 5.5}",2,7.1,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001164745,"{'14': 95.1, '36': 24.8, '15B': 24.3, '15C': 24.2, '09L': 23.4}",1,95.1,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901244575,"{'19A-I': 99.5, '19A-II': 97.3, '19A': 87.5, '19A-III': 87.3, '19AF': 61.7}",1,99.5,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(95.25)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001169325,"{'05': 95.2, '36': 20.2, '12A': 19.7, '45': 19.7, '46': 19.6}",1,95.2,,5,,,{},{},5,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001330575,"{'06E': 99.9, '06B-III': 97.4, '06B-I': 44.8, '06A-III': 44.3, '06B-II': 43.5}",1,99.9,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007784695,"{'01': 6.4, '25F': 6.1, '25A': 5.9, '36': 5.7, '38': 5.2}",2,6.4,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001174545,"{'06E': 100.0, '06B-III': 93.6, '06A-I': 42.6, '06B': 42.2, '06B-I': 41.1}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001152685,"{'20': 73.0, '35A': 23.2, '47F': 21.2, '09L': 19.9, '35C': 19.6}",1,73.0,,20,,,{},{},20,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001330535,"{'19F-I': 96.0, '19F': 95.7, '19F-III': 94.1, '19F-II': 92.9, '19F-IV': 88.9}",1,96.0,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001163305,"{'40': 99.6, '07B': 93.9, '07C': 75.4, '24F2': 48.2, '24F': 47.9}",1,99.6,,7B/40,,,{},{},7B/40,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001348355,"{'23F': 94.0, '23A': 63.5, '28A': 48.5, '23B': 47.0, '06A-IV': 47.0}",1,94.0,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001129165,"{'35F': 99.3, '47F': 74.6, '34': 26.7, '35B': 26.5, '29': 22.5}",1,99.3,,35F,,,{},{},35F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001114225,"{'19F-I': 95.7, '19F': 95.4, '19F-III': 93.9, '19F-II': 92.6, '19F-IV': 88.6}",1,95.7,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007785595,"{'01': 6.4, '45': 6.3, '25F': 5.7, '25A': 5.5, '22F': 5.2}",2,6.4,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171465,"{'06B-I': 99.4, '06A-III': 97.2, '06B-II': 89.8, '06A': 89.7, '06A-V': 87.9}",1,99.4,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(100.0)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001340235,"{'06A': 80.0, '06B-II': 78.5, '06A-III': 78.3, '06A-II': 77.9, '06A-VI': 77.9}",1,80.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[0]],{'wciN': ['a: 85.68']},{'wciN': 0},6A_6B_6C_6D,RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170605,"{'06B-I': 99.6, '06A-III': 97.5, '06B-II': 90.1, '06A': 89.7, '06A-IV': 88.9}",1,99.6,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(100.0)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001158285,"{'19F-I': 95.7, '19F': 95.4, '19F-III': 93.9, '19F-II': 92.6, '19F-IV': 88.6}",1,95.7,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001136765,"{'19F-I': 92.3, '19F': 91.9, '19F-III': 90.5, '19F-II': 89.1, '19F-IV': 85.1}",1,92.3,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_002265215,"{'06E': 99.6, '06B-III': 99.2, '06B-I': 46.9, '06A-III': 46.4, '06A-II': 45.4}",1,99.6,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001335975,"{'04': 98.2, '45': 32.8, '12F': 23.8, '44': 23.6, '12A': 22.7}",1,98.2,,4,,,{},{},4,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170255,"{'23F': 99.2, '23A': 65.5, '23B': 49.1, '28A': 48.1, '06A-IV': 47.2}",1,99.2,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007787365,"{'36': 10.6, '23B1': 6.7, '06A-IV': 6.5, '20': 5.8, '45': 5.8}",1,10.6,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001330115,"{'19F-I': 95.7, '19F': 95.4, '19F-III': 93.9, '19F-II': 92.6, '19F-IV': 88.6}",1,95.7,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001137825,"{'35B': 99.3, '33F': 33.6, '35C': 33.3, '34': 33.1, '35A': 32.9}",1,99.3,,35B/35D,,,{},{},35B/35D,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001346175,"{'38': 87.4, '25F': 83.8, '25A': 83.0, '36': 11.4, '20': 7.5}",1,87.4,25F_25A_38,25F_25A_38,,"[[0], [18]]","{'wcyD': ['b: 22.59'], 'wcyV': np.float64(4.69)}","{'wcyD': 0, 'wcyV': 'not_detected'}",25F_25A_38,RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_002866465,"{'45': 6.5, '01': 6.2, '25F': 5.6, '25A': 5.4, '22F': 5.3}",2,6.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001340135,"{'19F-I': 95.5, '19F': 95.2, '19F-III': 93.7, '19F-II': 92.4, '19F-IV': 88.4}",1,95.5,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907170335,"{'14': 91.8, '36': 27.4, '09L': 24.8, '09N': 23.9, '15B': 23.7}",1,91.8,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001174745,"{'36': 8.2, '06A-IV': 6.5, '01': 6.1, '20': 5.5, '06C': 5.3}",1,8.2,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001301415,"{'35B': 99.8, '33F': 33.7, '35C': 33.5, '34': 33.1, '35A': 33.1}",1,99.8,,35B/35D,,,{},{},35B/35D,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170455,"{'23F': 98.4, '23A': 65.3, '28A': 48.0, '06A': 45.5, '28F': 45.4}",1,98.4,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_010604165,"{'25F': 4.6, '25A': 4.5, '09L': 2.4, '01': 2.3, '36': 2.3}",1,4.6,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001163285,"{'19F': 93.5, '19F-I': 93.2, '19F-III': 91.9, '19F-II': 90.4, '19F-IV': 86.6}",1,93.5,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007785325,"{'01': 6.9, '45': 5.9, '25F': 5.8, '25A': 5.6, '38': 4.7}",3,6.9,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001084385,"{'21': 92.2, '22F': 34.4, '06A-IV': 34.3, '06A-II': 34.0, '06A-VI': 34.0}",1,92.2,,21,,,{},{},21,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170105,"{'06E': 99.8, '06B-III': 99.2, '06B-I': 46.8, '06A-III': 46.3, '06A-II': 45.4}",1,99.8,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907168655,"{'09A': 99.0, '09V': 98.8, '09N': 36.7, '09L': 34.8, '11F': 26.6}",1,99.0,,9A/9V,,,{},{},9A/9V,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001116625,"{'01': 4.9, '45': 3.9, '25F': 3.5, '25A': 3.4, '22F': 2.7}",1,4.9,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170935,"{'06D': 87.1, '06C': 85.1, '06C-I': 85.1, '06A-I': 76.0, '06B': 75.9}",1,87.1,6A_6B_6C_6D,6A_6B_6C_6D,,[[0]],{'wciN': ['b: 86.4']},{'wciN': 0},6A_6B_6C_6D,RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170765,"{'38': 89.6, '25F': 85.4, '25A': 84.6, '36': 11.8, '20': 7.9}",1,89.6,25F_25A_38,25F_25A_38,,"[[0], [18]]","{'wcyD': ['b: 22.59'], 'wcyV': np.float64(4.69)}","{'wcyD': 0, 'wcyV': 'not_detected'}",25F_25A_38,RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907170385,"{'14': 91.5, '36': 28.3, '15B': 24.1, '15C': 24.0, '09L': 23.9}",1,91.5,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171345,"{'06B-I': 99.3, '06A-III': 97.1, '06B-II': 89.7, '06A': 89.6, '06A-V': 87.8}",1,99.3,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(100.0)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907170005,"{'14': 92.3, '36': 28.3, '09L': 24.3, '15B': 24.2, '15C': 24.1}",1,92.3,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000946055,"{'21': 92.2, '22F': 34.8, '06A-IV': 34.3, '06A-II': 34.0, '06A-VI': 34.0}",1,92.2,,21,,,{},{},21,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_923172305,{45: 0.1},1,0.1,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001098325,"{'01': 5.4, '25F': 5.2, '25A': 5.0, '38': 4.3, '45': 4.0}",1,5.4,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170475,"{'19F-I': 99.9, '19F': 96.9, '19F-III': 96.9, '19F-II': 94.1, '19F-IV': 89.5}",1,99.9,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001153025,"{'45': 5.2, '25F': 4.3, '25A': 4.1, '36': 3.9, '06C-I': 3.9}",2,5.2,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001107925,"{'06E': 99.9, '06B-III': 95.5, '06B-I': 42.9, '06A-I': 42.6, '06A-III': 42.4}",1,99.9,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001171045,"{'36': 7.2, '20': 6.6, '25F': 4.7, '25A': 4.5, '45': 4.3}",1,7.2,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000334695,"{'01': 99.5, '19F': 32.3, '19F-I': 31.8, '19F-III': 31.6, '19F-II': 31.3}",1,99.5,,1,,,{},{},1,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001132165,"{'15C': 96.3, '15B': 96.1, '15A': 61.5, '15F': 47.8, '23A': 34.7}",1,96.3,,15B/15C,,,{},{},15B/15C,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170835,"{'19F-I': 92.5, '19F-III': 90.1, '19F': 89.5, '19F-II': 86.9, '19F-IV': 85.0}",1,92.5,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171195,"{'06B-I': 99.6, '06A-III': 97.5, '06B-II': 90.2, '06A': 89.8, '06A-V': 88.3}",1,99.6,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(100.0)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001104845,"{'23F': 93.1, '23A': 63.3, '06A-IV': 53.3, '06B-II': 51.9, '23B': 50.9}",1,93.1,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001581235,"{'25F': 7.5, '25A': 7.3, '45': 6.4, '01': 5.9, '22F': 5.4}",2,7.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001146285,"{'22A': 94.2, '22F': 76.9, '06A-IV': 45.6, '06A-II': 43.9, '06B-I': 43.9}",1,94.2,,22A,,,{},{},22A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001909225,"{'03': 95.2, '36': 16.7, '20': 15.4, '09L': 13.7, '09N': 13.6}",1,95.2,,3,,,{},{},3,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_020038075,"{'16F': 44.6, '23A': 42.4, '23B': 40.4, '23F': 31.8, '18A': 30.5}",1,44.6,,"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",,,{},{},"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001193295,"{'14': 94.6, '15B': 24.2, '15C': 24.1, '09L': 23.3, '19F-II': 22.4}",1,94.6,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907168725,"{'19A': 100.0, '19A-III': 99.8, '19A-I': 86.2, '19A-II': 84.0, '19AF': 57.2}",1,100.0,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(100.0)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000355925,"{'01': 91.4, '19F': 32.3, '19F-I': 31.8, '19F-III': 31.6, '19F-II': 31.3}",1,91.4,,1,,,{},{},1,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001148645,"{'22A': 94.2, '22F': 77.0, '06A-IV': 45.5, '06A-II': 43.8, '06B-I': 43.8}",1,94.2,,22A,,,{},{},22A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001581555,"{'14': 89.4, '19F-IV': 25.9, '36': 25.4, '09L': 24.8, '09N': 24.6}",1,89.4,,14,,,{},{},14,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170755,"{'06C-I': 99.6, '06C': 99.4, '06D': 84.6, '06A-II': 79.2, '06A-VI': 79.2}",1,99.6,6A_6B_6C_6D,6A_6B_6C_6D,,[[2]],"{'wciN': ['b', np.float64(91.3)]}",{'wciN': 'b'},6C/6D,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001205875,"{'01': 99.3, '35B': 99.3, '06C': 43.8, '06C-I': 43.8, '06B-I': 43.4}",1,99.3,,"Mixed serotypes- {'1', '35B/35D'}",,,{},{},"Mixed serotypes- {'1', '35B/35D'}",AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001146585,"{'19F-I': 95.9, '19F': 95.6, '23F': 95.5, '19F-III': 94.1, '19F-II': 92.8}",1,95.9,,"Mixed serotypes- {'19F', '23F'}",,,{},{},"Mixed serotypes- {'19F', '23F'}",AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001199715,"{'14': 89.9, '36': 28.7, '09L': 22.8, '19F-II': 22.2, '09N': 21.7}",1,89.9,,14,,,{},{},14,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900193405,"{'35F': 99.3, '47F': 74.6, '34': 26.7, '35B': 25.4, '29': 22.0}",1,99.3,,35F,,,{},{},35F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900043105,"{'15A': 43.2, '15F': 32.2, '15C': 27.6, '15B': 27.5, '23F': 14.3}",1,43.2,,"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",,,{},{},"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170995,"{'19F-III': 100.0, '19F': 98.0, '19F-I': 97.3, '19F-II': 94.8, '19F-IV': 89.5}",1,100.0,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007786875,"{'01': 7.0, '45': 6.4, '25F': 5.8, '25A': 5.6, '22F': 4.9}",2,7.0,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001097405,"{'19F': 69.1, '19F-I': 68.8, '19F-II': 68.3, '19F-III': 67.8, '19F-IV': 65.3}",1,69.1,,"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",,,{},{},"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_009721155,"{'22F': 98.5, '22A': 73.5, '23A': 46.2, '06A-IV': 44.1, '23F': 43.6}",1,98.5,,22F,,,{},{},22F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901260595,"{'06A-I': 96.1, '06B': 92.0, '06A-V': 86.8, '06A': 85.0, '06A-III': 83.4}",1,96.1,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(96.61)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001136965,"{'13': 98.7, '09L': 27.3, '09N': 27.0, '14': 26.5, '20': 25.9}",1,98.7,,13,,,{},{},13,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001129485,"{'19F-I': 95.5, '19F': 95.2, '19F-III': 93.7, '19F-II': 92.4, '19F-IV': 88.4}",1,95.5,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001168665,"{'35B': 99.7, '33F': 33.7, '35C': 33.5, '34': 33.3, '35A': 33.1}",1,99.7,,35B/35D,,,{},{},35B/35D,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901235725,"{'06E': 100.0, '06B-III': 98.8, '06B-I': 46.3, '06A-III': 45.8, '06A-II': 44.8}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900172195,"{'23F': 96.5, '23A': 63.2, '06A-IV': 48.6, '23B': 48.4, '28A': 47.2}",1,96.5,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001138545,"{'19B': 91.7, '19C': 70.5, '19F-II': 49.3, '19F-IV': 49.3, '19F-I': 48.5}",1,91.7,,19B,,,{},{},19B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001330595,"{'19F-I': 95.7, '19F': 95.4, '19F-III': 93.9, '19F-II': 92.6, '19F-IV': 88.6}",1,95.7,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001581535,"{'16F': 67.2, '28F': 39.5, '28A': 37.5, '18F': 30.9, '18A': 30.1}",1,67.2,,"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",,,{},{},"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001157605,"{'19F-I': 96.0, '19F': 95.7, '19F-III': 94.1, '19F-II': 92.9, '19F-IV': 88.9}",1,96.0,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001346855,"{'45': 6.9, '01': 5.9, '25F': 5.7, '25A': 5.5, '38': 4.6}",3,6.9,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001173905,"{'36': 9.4, '23B1': 5.7, '20': 5.6, '45': 5.5, '06B-I': 5.5}",1,9.4,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007784915,"{'01': 6.7, '45': 5.9, '25F': 5.7, '20': 5.5, '25A': 5.5}",3,6.7,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_003934465,"{'15C': 71.1, '15B': 71.0, '15A': 48.1, '15F': 37.7, '23A': 33.7}",1,71.1,,15B/15C,,,{},{},15B/15C,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001104385,"{'10A': 99.3, '10B': 67.0, '10C': 27.7, '10F': 18.1, '06B-I': 15.2}",1,99.3,,10A,,,{},{},10A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_012911375,"{'35B': 79.6, '33F': 33.3, '34': 33.3, '35C': 33.2, '35A': 32.8}",1,79.6,,35B/35D,,,{},{},35B/35D,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170815,"{'15C': 93.7, '15B': 93.6, '15A': 62.0, '15F': 48.5, '14': 33.0}",1,93.7,,15B/15C,,,{},{},15B/15C,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907167325,"{'19F-II': 99.5, '19F': 95.3, '19F-III': 94.3, '19F-I': 94.0, '19F-IV': 93.2}",1,99.5,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001113585,"{'06A': 89.6, '06A-III': 89.2, '06B-I': 87.9, '06B-II': 87.7, '06A-II': 87.2}",1,89.6,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(100.0)]}",{'wciN': 'a'},6A/6B,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001136365,"{'38': 88.0, '25F': 84.2, '25A': 83.4, '36': 11.8, '20': 7.4}",1,88.0,25F_25A_38,25F_25A_38,,"[[0], [18]]","{'wcyD': ['b: 22.59'], 'wcyV': np.float64(4.69)}","{'wcyD': 0, 'wcyV': 'not_detected'}",25F_25A_38,RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001206515,"{'06B-III': 67.7, '06E': 66.2, '06B-I': 33.6, '06A-IV': 33.0, '06A-III': 32.7}",1,67.7,,"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",,,{},{},"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007785395,"{'36': 10.7, '23B1': 6.8, '06A-IV': 6.6, '45': 6.1, '20': 6.0}",1,10.7,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001165045,"{'35B': 43.1, '33B': 40.2, '33D': 36.1, '34': 31.3, '22F': 30.1}",1,43.1,,"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",,,{},{},"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001149945,"{'35B': 99.5, '33F': 33.4, '35C': 33.3, '34': 32.9, '35A': 32.9}",1,99.5,,35B/35D,,,{},{},35B/35D,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907166855,"{'09A': 89.7, '09V': 89.5, '09N': 34.0, '09L': 32.6, '11F': 26.6}",1,89.7,,9A/9V,,,{},{},9A/9V,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170725,"{'13': 98.9, '19F-I': 98.1, '19F': 95.5, '19F-III': 95.5, '19F-II': 93.9}",1,98.9,,"Mixed serotypes- {'19F', '13'}",,,{},{},"Mixed serotypes- {'19F', '13'}",AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_012911125,"{'35B': 64.9, '33F': 33.3, '34': 33.3, '35C': 33.2, '35A': 32.8}",1,64.9,,"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",,,{},{},"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001200955,"{'04': 98.2, '45': 32.7, '12F': 23.8, '44': 23.6, '12A': 22.7}",1,98.2,,4,,,{},{},4,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_019446745,"{'38': 97.1, '25F': 82.5, '25A': 81.6, '36': 10.4, '20': 6.4}",1,97.1,25F_25A_38,25F_25A_38,,"[[9], [19]]","{'wcyD': ['b', np.float64(100.0)], 'wcyV': np.float64(100.0)}","{'wcyD': 'b', 'wcyV': 'detected'}",38,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001157525,"{'19F-I': 95.7, '19F': 95.4, '19F-III': 93.9, '19F-II': 92.6, '19F-IV': 88.6}",1,95.7,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001330355,"{'19F-I': 92.2, '19F': 91.7, '19F-III': 90.3, '19F-II': 89.4, '19F-IV': 85.4}",1,92.2,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001149925,"{'19F-I': 91.7, '19F': 91.4, '19F-III': 90.4, '19F-II': 88.6, '19F-IV': 84.6}",1,91.7,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007784925,"{'36': 10.8, '23B1': 6.8, '06A-IV': 6.7, '45': 6.6, '20': 6.0}",1,10.8,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007784865,"{'45': 5.9, '01': 5.8, '25F': 5.7, '20': 5.5, '25A': 5.5}",2,5.9,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001336735,"{'45': 5.1, '20': 5.0, '25F': 5.0, '25A': 4.9, '22F': 4.6}",2,5.1,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_002016615,"{'22F': 97.5, '22A': 73.4, '06A': 42.6, '06B': 42.1, '06A-II': 41.9}",1,97.5,,22F,,,{},{},22F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001340555,"{'13': 83.6, '36': 25.5, '14': 25.2, '09L': 24.6, '09N': 24.5}",1,83.6,,13,,,{},{},13,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001172625,"{'14': 79.9, '19F': 56.5, '19F-I': 56.3, '19F-II': 55.2, '19F-III': 55.1}",1,79.9,,14,,,{},{},14,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170295,"{'19A-I': 99.7, '19A-II': 97.5, '19A': 87.7, '19A-III': 87.5, '19AF': 61.8}",1,99.7,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(95.25)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000385715,"{'23F': 96.9, '23A': 65.6, '28A': 47.0, '23B': 46.0, '06A': 45.9}",1,96.9,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007787455,"{'01': 6.8, '45': 5.8, '25F': 5.7, '25A': 5.5, '20': 5.1}",2,6.8,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001154545,"{'19F-II': 99.6, '19F': 95.4, '19F-III': 94.4, '19F-I': 94.1, '19F-IV': 93.3}",1,99.6,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171175,"{'19F-I': 99.8, '19F': 96.8, '19F-III': 96.8, '19F-II': 94.0, '19F-IV': 89.4}",1,99.8,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900028255,"{'06B-I': 99.7, '06A-III': 97.6, '06B-II': 90.2, '06A': 89.8, '06A-V': 88.3}",1,99.7,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(100.0)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171255,"{'06A-I': 100.0, '06B': 94.5, '06A-V': 89.3, '06A': 87.1, '06A-III': 86.0}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(96.61)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001330855,"{'19F-I': 95.8, '19F': 95.5, '19F-III': 93.9, '19F-II': 92.7, '19F-IV': 88.7}",1,95.8,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001157745,"{'22F': 63.3, '22A': 46.8, '06D': 25.2, '06A': 25.0, '35B': 24.1}",1,63.3,,"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",,,{},{},"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001169545,"{'06D': 77.1, '06C': 77.0, '06C-I': 77.0, '06A': 67.6, '06B-I': 66.0}",1,77.1,6A_6B_6C_6D,6A_6B_6C_6D,,[[0]],{'wciN': ['b: 83.5']},{'wciN': 0},6A_6B_6C_6D,RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001116045,"{'19A': 100.0, '19A-III': 99.8, '19A-I': 86.2, '19A-II': 83.7, '19AF': 57.2}",1,100.0,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(100.0)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001142405,"{'19F-I': 95.3, '19F': 95.0, '19F-III': 93.5, '19F-II': 92.2, '19F-IV': 88.2}",1,95.3,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001162905,"{'19F-I': 93.6, '19F': 93.3, '19F-III': 91.8, '19F-II': 90.5, '19F-IV': 86.5}",1,93.6,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907168555,"{'19A': 99.9, '19A-III': 99.7, '19A-I': 86.1, '19A-II': 83.6, '19AF': 57.2}",1,99.9,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(100.0)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000173635,"{'14': 99.9, '36': 26.0, '09L': 24.4, '15B': 24.3, '15C': 24.2}",1,99.9,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001134045,"{'10F': 98.2, '10C': 80.9, '10B': 22.4, '10A': 19.2, '22F': 14.4}",1,98.2,,10F,,,{},{},10F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001114785,"{'45': 6.3, '01': 6.0, '25F': 5.7, '25A': 5.5, '36': 5.1}",2,6.3,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907168605,"{'19A': 99.8, '19A-III': 99.6, '19A-I': 86.0, '19A-II': 83.5, '19AF': 57.0}",1,99.8,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(100.0)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901244445,"{'12F': 96.3, '44': 93.3, '12B': 93.2, '12A': 84.7, '46': 81.6}",1,96.3,12F_12A_12B_44_46,12F_12A_12B_44_46,,[[5]],"{'wciI': [2, np.float64(94.56)]}",{'wciI': 2},12F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000385755,"{'06E': 87.7, '06B-III': 85.9, '06B-I': 50.6, '06A-III': 50.0, '06A-II': 49.6}",1,87.7,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007786675,"{'45': 6.2, '01': 5.8, '25F': 5.8, '25A': 5.6, '22F': 5.4}",2,6.2,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001129665,"{'36': 12.7, '20': 8.1, '06A-IV': 7.6, '06C': 6.2, '06B-I': 6.2}",1,12.7,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_012911465,"{'35B': 81.4, '34': 33.3, '33F': 33.0, '35C': 32.9, '35A': 32.5}",1,81.4,,35B/35D,,,{},{},35B/35D,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_002249745,"{'01': 7.4, '45': 6.6, '20': 5.9, '25F': 5.8, '25A': 5.6}",7,7.4,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001096845,"{'36': 10.2, '20': 5.6, '06C': 5.4, '06C-I': 5.4, '06B-I': 5.3}",1,10.2,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007785555,"{'01': 7.5, '45': 6.5, '25F': 5.8, '25A': 5.6, '38': 4.9}",3,7.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001126785,"{'06E': 100.0, '06B-III': 97.5, '06B-I': 44.8, '06A-III': 44.3, '06B-II': 43.5}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000762825,"{'19A': 99.4, '19A-III': 99.2, '19A-I': 86.1, '19A-II': 83.6, '19AF': 57.2}",1,99.4,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(100.0)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007787145,"{'01': 7.2, '25F': 6.6, '45': 6.5, '25A': 6.4, '22F': 6.1}",2,7.2,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001335355,"{'04': 98.3, '45': 31.8, '12F': 23.8, '44': 23.6, '12A': 22.7}",1,98.3,,4,,,{},{},4,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170805,"{'14': 99.7, '09L': 27.0, '36': 26.1, '15B': 24.3, '09N': 24.2}",1,99.7,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907167935,"{'14': 91.1, '36': 26.2, '09L': 25.3, '09N': 24.7, '15B': 23.4}",1,91.1,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001581405,"{'01': 27.0, '06C': 20.9, '06C-I': 20.9, '06A-II': 20.0, '06A-V': 20.0}",1,27.0,,"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",,,{},{},"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_012911335,"{'35B': 78.0, '33F': 33.3, '34': 33.3, '35C': 33.2, '35A': 32.8}",1,78.0,,35B/35D,,,{},{},35B/35D,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901247265,"{'19A-I': 99.4, '19A-II': 97.7, '19A': 88.0, '19A-III': 87.8, '19AF': 62.0}",1,99.4,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(95.25)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901246035,"{'19A-I': 99.4, '19A-II': 97.7, '19A': 88.0, '19A-III': 87.8, '19AF': 62.0}",1,99.4,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(95.25)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001117505,"{'06E': 100.0, '06B-III': 99.6, '06B-I': 47.0, '06A-III': 46.5, '06A-II': 45.5}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907168755,"{'19A': 96.4, '19A-III': 96.2, '19A-II': 83.2, '19A-I': 82.8, '19AF': 56.8}",1,96.4,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(100.0)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001330695,"{'06E': 100.0, '06B-III': 93.3, '06A-I': 42.6, '06B': 42.2, '06B-I': 40.9}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_009721145,"{'21': 99.4, '22F': 41.6, '06A-IV': 41.1, '06A-II': 40.7, '06A-VI': 40.6}",1,99.4,,21,,,{},{},21,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900027335,"{'12A': 4.5, '46': 4.5, '06A-IV': 2.2, '01': 1.8, '22F': 1.5}",1,4.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001132745,"{'36': 6.4, '06A-IV': 5.7, '20': 5.1, '06C-I': 4.1, '06C': 4.0}",1,6.4,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001337295,"{'19F-I': 95.8, '19F': 95.5, '19F-III': 93.9, '19F-II': 92.7, '19F-IV': 88.7}",1,95.8,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170435,"{'19F-I': 99.7, '19F': 96.7, '19F-III': 96.7, '19F-II': 93.9, '19F-IV': 89.3}",1,99.7,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001136505,"{'19A': 99.3, '19A-III': 99.1, '19A-I': 86.2, '19A-II': 83.9, '19AF': 57.2}",1,99.3,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(100.0)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907168745,"{'09A': 99.7, '09V': 99.5, '06E': 90.3, '06B-III': 86.7, '06A-III': 54.3}",1,99.7,,"Mixed serotypes- {'9A/9V', '6A_6B_6C_6D'}",,,{},{},"Mixed serotypes- {'9A/9V', '6A_6B_6C_6D'}",AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007785475,"{'36': 10.8, '06A-IV': 6.7, '45': 6.3, '20': 6.0, '06B-I': 5.5}",1,10.8,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171355,"{'35F': 99.4, '47F': 74.2, '34': 26.4, '35B': 26.4, '36': 22.6}",1,99.4,,35F,,,{},{},35F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001094665,"{'06E': 96.5, '06B-III': 94.9, '06B-I': 44.9, '06A-III': 44.4, '06B-II': 43.8}",1,96.5,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001334715,"{'04': 98.3, '45': 30.7, '12F': 23.8, '44': 23.6, '12A': 22.7}",1,98.3,,4,,,{},{},4,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907168715,"{'19A': 100.0, '19A-III': 99.8, '19A-I': 86.2, '19A-II': 83.7, '19AF': 57.2}",1,100.0,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(100.0)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007787375,"{'01': 6.9, '45': 6.2, '20': 5.7, '25F': 5.7, '25A': 5.5}",3,6.9,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001715925,"{'01': 73.3, '19F': 31.2, '19F-I': 30.7, '19F-III': 30.5, '19F-II': 30.2}",1,73.3,,1,,,{},{},1,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001301775,"{'15C': 95.8, '15B': 95.7, '15A': 61.2, '15F': 47.6, '23A': 34.7}",1,95.8,,15B/15C,,,{},{},15B/15C,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001101665,"{'36': 11.2, '06A-IV': 7.2, '20': 6.5, '06C': 6.0, '06C-I': 6.0}",1,11.2,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001098365,"{'13': 98.9, '09L': 28.5, '09N': 28.1, '20': 28.1, '14': 27.0}",1,98.9,,13,,,{},{},13,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001097305,"{'06C-I': 99.9, '06C': 99.7, '06D': 84.6, '06A-II': 79.6, '06A-VI': 79.6}",1,99.9,6A_6B_6C_6D,6A_6B_6C_6D,,[[2]],"{'wciN': ['b', np.float64(91.3)]}",{'wciN': 'b'},6C/6D,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001174325,"{'19F-I': 95.6, '19F': 95.3, '19F-III': 93.8, '19F-II': 92.5, '19F-IV': 88.5}",1,95.6,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901320925,"{'34': 97.8, '33F2': 35.2, '35B': 33.5, '33F': 29.8, '33C': 28.5}",1,97.8,,34,,,{},{},34,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007787135,"{'01': 6.6, '45': 6.3, '25F': 5.6, '25A': 5.4, '22F': 5.2}",4,6.6,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171625,"{'19F-III': 98.4, '19F': 98.0, '19F-I': 98.0, '19F-II': 93.8, '19F-IV': 89.2}",1,98.4,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001095725,"{'23F': 94.0, '23A': 63.5, '28A': 48.5, '23B': 47.0, '06A-III': 46.4}",1,94.0,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001139965,"{'23F': 93.8, '23A': 63.4, '28A': 48.4, '23B': 47.0, '06A-III': 46.3}",1,93.8,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171015,"{'19F-I': 99.5, '19F': 96.5, '19F-III': 96.5, '19F-II': 93.7, '19F-IV': 89.1}",1,99.5,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001330675,"{'06E': 100.0, '06B-III': 95.5, '06B-I': 42.8, '06A-I': 42.6, '06A-III': 42.3}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001138285,"{'06E': 100.0, '06B-III': 98.4, '06B-I': 45.9, '06A-III': 45.4, '06A-II': 44.4}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171685,"{'06B-I': 99.7, '06A-III': 97.6, '06B-II': 90.3, '06A': 89.8, '06A-V': 88.4}",1,99.7,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(100.0)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001581455,"{'45': 6.3, '01': 6.1, '22F': 5.2, '20': 4.7, '38': 4.6}",3,6.3,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901249135,"{'06A-II': 93.8, '06A-VI': 93.8, '06B-II': 88.3, '06A-V': 87.9, '06A-III': 86.9}",1,93.8,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(93.22)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001329195,"{'19F-I': 96.0, '19F': 95.7, '19F-III': 94.1, '19F-II': 92.9, '19F-IV': 88.9}",1,96.0,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001107345,"{'36': 5.5, '25F': 4.4, '25A': 4.3, '20': 4.0, '06C-I': 3.5}",1,5.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_008039055,"{'03': 97.4, '01': 16.4, '20': 15.4, '09N': 15.3, '09L': 15.1}",1,97.4,,3,,,{},{},3,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001344575,"{'19A-I': 99.3, '19A-II': 97.7, '19A': 87.9, '19A-III': 87.7, '19AF': 62.0}",1,99.3,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(95.25)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907170155,"{'14': 91.6, '36': 27.5, '15B': 23.7, '09L': 23.6, '15C': 23.6}",1,91.6,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_002889035,"{'19F-I': 95.7, '19F': 95.4, '19F-III': 93.9, '19F-II': 92.6, '19F-IV': 88.6}",1,95.7,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001136985,"{'36': 10.9, '06A-IV': 7.0, '20': 6.7, '06B-I': 5.9, '06C': 5.7}",1,10.9,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001347875,"{'10A': 99.1, '10B': 67.0, '10C': 27.7, '10F': 18.1, '06B-I': 15.2}",1,99.1,,10A,,,{},{},10A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001210005,"{'36': 10.7, '06A-IV': 7.9, '20': 6.7, '06B-I': 6.7, '06C': 6.6}",1,10.7,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_002866265,"{'01': 6.5, '45': 6.4, '25F': 5.6, '25A': 5.5, '22F': 5.2}",3,6.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001128205,"{'01': 5.3, '20': 5.1, '25F': 4.9, '25A': 4.8, '45': 4.6}",2,5.3,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001300035,"{'19F-I': 96.0, '19F': 95.7, '19F-III': 94.1, '19F-II': 92.9, '19F-IV': 88.9}",1,96.0,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001581305,"{'19A-I': 93.3, '19A-II': 91.7, '19A': 82.4, '19A-III': 82.2, '19AF': 56.8}",1,93.3,19A_19AF,19A_19AF,,[[0]],{'wzy': ['1: 67.97']},{'wzy': 0},19A_19AF,RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001330815,"{'19F-I': 95.8, '19F': 95.5, '19F-III': 93.9, '19F-II': 92.7, '19F-IV': 88.7}",1,95.8,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001909235,"{'03': 95.2, '36': 17.3, '20': 15.7, '01': 14.9, '14': 14.2}",1,95.2,,3,,,{},{},3,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007785015,"{'01': 6.4, '45': 5.9, '25F': 5.7, '20': 5.5, '25A': 5.5}",3,6.4,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001925225,"{'06E': 99.7, '06B-III': 95.6, '06B-I': 43.1, '06A-III': 42.9, '06A-I': 42.7}",1,99.7,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007784685,"{'01': 6.6, '45': 6.3, '25F': 5.7, '25A': 5.5, '38': 4.7}",1,6.6,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170875,"{'23F': 99.1, '23A': 65.2, '23B': 47.7, '28A': 47.6, '06A-V': 45.5}",1,99.1,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171285,"{'14': 77.2, '36': 23.8, '15B': 21.4, '15C': 21.3, '09L': 21.1}",1,77.2,,14,,,{},{},14,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001157045,"{'06E': 100.0, '06B-III': 96.2, '06B-I': 43.7, '06A-III': 43.2, '06A-I': 42.6}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901339955,"{'04': 99.7, '45': 33.1, '12F': 23.5, '44': 23.3, '12A': 22.4}",1,99.7,,4,,,{},{},4,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001072515,"{'03': 95.2, '36': 17.0, '20': 14.9, '14': 13.6, '09L': 13.3}",1,95.2,,3,,,{},{},3,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_003934115,"{'23B': 80.1, '23B1': 53.2, '23F': 38.1, '28A': 33.1, '06B-I': 32.9}",1,80.1,,23B,,,{},{},23B,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001337175,"{'36': 5.0, '20': 4.7, '45': 4.0, '06C-I': 3.9, '06C': 3.8}",1,5.0,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901250965,"{'19F-I': 98.0, '19F': 97.3, '19F-III': 96.8, '19F-II': 95.3, '19F-IV': 90.4}",1,98.0,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007784775,"{'01': 7.1, '45': 5.9, '25F': 5.7, '20': 5.5, '25A': 5.5}",4,7.1,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_010604205,"{'20': 4.6, '22F': 4.4, '45': 4.0, '25A': 3.5, '25F': 3.5}",1,4.6,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907171665,"{'06E': 94.8, '14': 92.5, '06B-III': 91.3, '06A-I': 45.6, '06A-V': 45.5}",1,94.8,,"Mixed serotypes- {'14', '6A_6B_6C_6D'}",,,{},{},"Mixed serotypes- {'14', '6A_6B_6C_6D'}",AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001174845,"{'19F-I': 95.5, '19F': 95.2, '19F-III': 93.7, '19F-II': 92.4, '19F-IV': 88.4}",1,95.5,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001910205,"{'03': 95.2, '36': 16.9, '20': 15.2, '09L': 13.6, '14': 13.6}",1,95.2,,3,,,{},{},3,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001098405,"{'34': 79.9, '33F2': 32.3, '35B': 30.6, '33F': 28.2, '33A': 26.6}",1,79.9,,34,,,{},{},34,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007787535,"{'01': 6.3, '45': 6.2, '25F': 5.7, '25A': 5.5, '22F': 5.0}",2,6.3,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001205235,"{'35A': 99.9, '35C': 85.2, '42': 84.6, '33A': 42.9, '33F': 42.6}",1,99.9,,35A/35C/42,,,{},{},35A/35C/42,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007785235,"{'01': 7.1, '45': 6.5, '25F': 5.8, '25A': 5.6, '22F': 5.5}",4,7.1,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001334135,"{'36': 10.1, '06A-IV': 6.8, '20': 5.9, '06B-I': 5.6, '06C': 5.4}",1,10.1,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000334615,"{'01': 99.1, '19F': 32.3, '19F-I': 31.8, '19F-III': 31.6, '19F-II': 31.3}",1,99.1,,1,,,{},{},1,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170275,"{'23F': 99.2, '23A': 65.4, '23B': 49.0, '28A': 48.1, '06A-IV': 47.3}",1,99.2,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171305,"{'06A-II': 99.7, '06A-VI': 99.7, '06B-II': 91.5, '06A-V': 90.7, '06A-III': 89.3}",1,99.7,6A_6B_6C_6D,6A_6B_6C_6D,,[[0]],{'wciN': ['a: 89.84']},{'wciN': 0},6A_6B_6C_6D,RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007787055,"{'01': 7.1, '45': 6.4, '25F': 5.8, '25A': 5.6, '22F': 5.3}",5,7.1,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171435,"{'19F-II': 94.1, '19F-IV': 93.8, '19F': 91.4, '19F-I': 90.1, '19F-III': 89.4}",1,94.1,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001345375,"{'15C': 87.7, '15B': 87.6, '15A': 64.5, '15F': 49.9, '23A': 30.2}",1,87.7,,15B/15C,,,{},{},15B/15C,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907169375,"{'14': 92.6, '36': 28.6, '09L': 24.4, '15B': 24.2, '15C': 24.1}",1,92.6,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001171305,"{'38': 88.9, '25F': 85.2, '25A': 84.3, '36': 11.9, '20': 8.4}",1,88.9,25F_25A_38,25F_25A_38,,"[[0], [18]]","{'wcyD': ['b: 22.59'], 'wcyV': np.float64(4.69)}","{'wcyD': 0, 'wcyV': 'not_detected'}",25F_25A_38,RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171245,"{'16F': 96.8, '19F-IV': 44.8, '19F-II': 44.0, '19F': 43.0, '19F-I': 42.4}",1,96.8,,16F,,,{},{},16F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001107545,"{'33C': 88.4, '34': 29.9, '35B': 26.4, '33F2': 23.6, '33F': 23.0}",1,88.4,,33C,,,{},{},33C,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907172125,"{'14': 91.4, '36': 28.0, '09L': 24.2, '15B': 23.5, '15C': 23.4}",1,91.4,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170925,"{'34': 98.7, '33F2': 35.4, '35B': 33.4, '33F': 30.0, '33C': 28.7}",1,98.7,,34,,,{},{},34,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001094605,"{'06E': 100.0, '06B-III': 99.6, '06B-I': 47.0, '06A-III': 46.5, '06A-II': 45.5}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001334635,"{'36': 10.9, '06A-IV': 7.4, '20': 7.2, '06C': 6.0, '06C-I': 6.0}",2,10.9,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171035,"{'18C': 99.4, '18B': 99.3, '18F': 75.3, '18A': 62.1, '16F': 38.9}",1,99.4,,18C/18B,,,{},{},18C/18B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001329535,"{'06E': 100.0, '06B-III': 94.5, '06A-I': 42.6, '06B': 42.2, '06B-I': 41.9}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001088925,"{'36': 6.0, '20': 5.9, '45': 5.5, '25F': 4.9, '25A': 4.7}",2,6.0,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001100385,"{'19F-I': 95.7, '19F': 95.4, '19F-III': 93.9, '19F-II': 92.6, '19F-IV': 88.6}",1,95.7,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007784785,"{'36': 10.5, '23B1': 6.6, '20': 5.7, '45': 5.7, '06A-IV': 5.2}",1,10.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_019446265,"{'01': 6.7, '22F': 5.1, '20': 5.0, '25F': 4.9, '25A': 4.7}",2,6.7,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171455,"{'06B-I': 99.3, '06A-III': 97.1, '06B-II': 89.7, '06A': 89.6, '06A-V': 87.8}",1,99.3,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(100.0)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171615,"{'23F': 97.8, '23A': 63.3, '23B': 48.4, '28A': 48.3, '06A-IV': 47.0}",1,97.8,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001124745,"{'19F-I': 95.5, '19F': 95.2, '19F-III': 93.7, '19F-II': 92.4, '19F-IV': 88.4}",1,95.5,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170395,"{'23F': 97.8, '23A': 63.3, '23B': 48.4, '28A': 48.3, '06A-IV': 47.0}",1,97.8,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_020038025,"{'15C': 95.8, '15B': 95.7, '15A': 68.0, '15F': 58.1, '23A': 42.0}",1,95.8,,15B/15C,,,{},{},15B/15C,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001099385,"{'19F': 79.0, '19F-I': 79.0, '19F-III': 77.9, '19F-II': 76.7, '19F-IV': 72.6}",1,79.0,,19F,,,{},{},19F,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001090245,"{'19F-I': 94.1, '19F': 93.8, '19F-III': 92.3, '19F-II': 91.0, '19F-IV': 87.0}",1,94.1,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901252165,"{'03': 97.4, '01': 17.8, '20': 15.5, '09N': 15.3, '09L': 15.1}",1,97.4,,3,,,{},{},3,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001155845,"{'19F-I': 95.8, '19F': 95.5, '19F-III': 93.9, '19F-II': 92.7, '19F-IV': 88.7}",1,95.8,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900172205,"{'19F-I': 96.0, '19F': 95.7, '19F-III': 94.1, '19F-II': 92.9, '19F-IV': 88.9}",1,96.0,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007785035,"{'45': 6.3, '25F': 5.8, '25A': 5.6, '01': 5.5, '22F': 4.8}",2,6.3,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900190865,"{'35F': 99.3, '47F': 74.6, '34': 26.7, '35B': 26.3, '29': 22.5}",1,99.3,,35F,,,{},{},35F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_019446295,"{'35B': 99.3, '33F': 33.4, '35C': 33.1, '34': 32.8, '35A': 32.7}",1,99.3,,35B/35D,,,{},{},35B/35D,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901239795,"{'23F': 91.1, '23A': 59.7, '06A-IV': 47.0, '28A': 46.8, '23B': 46.3}",1,91.1,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007787725,"{'25F': 7.8, '25A': 7.6, '45': 6.4, '01': 6.2, '22F': 5.4}",3,7.8,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001581295,"{'01': 27.2, '06C': 21.0, '06C-I': 21.0, '06A-II': 20.1, '06A-V': 20.1}",1,27.2,,"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",,,{},{},"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001135225,"{'19F-I': 91.5, '19F': 91.2, '19F-III': 89.7, '19F-II': 88.6, '19F-IV': 84.6}",1,91.5,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001162485,"{'36': 11.2, '23B1': 7.2, '06A-IV': 6.7, '20': 6.1, '45': 5.6}",1,11.2,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001334055,"{'01': 6.5, '45': 6.3, '25F': 5.6, '25A': 5.4, '22F': 4.8}",1,6.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001719775,"{'14': 80.2, '36': 26.8, '09L': 25.4, '09N': 24.8, '15B': 23.7}",1,80.2,,14,,,{},{},14,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007785485,"{'45': 6.1, '25F': 5.8, '25A': 5.6, '22F': 5.2, '38': 4.9}",2,6.1,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_003934105,"{'23B': 73.7, '23B1': 49.5, '23F': 36.9, '06A-IV': 33.9, '06B-I': 32.3}",1,73.7,,23B,,,{},{},23B,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001159265,"{'20': 5.4, '22F': 5.1, '25F': 4.5, '25A': 4.4, '45': 4.4}",1,5.4,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001155965,"{'19F': 88.4, '19F-I': 88.3, '19F-III': 86.8, '19F-II': 85.5, '19F-IV': 82.1}",1,88.4,,19F,,,{},{},19F,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001715865,"{'09A': 98.0, '09V': 97.8, '09N': 37.6, '09L': 36.6, '11F': 27.1}",1,98.0,,9A/9V,,,{},{},9A/9V,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001173345,"{'19F': 86.3, '19F-I': 86.1, '19F-III': 84.3, '19F-II': 83.2, '19F-IV': 79.2}",1,86.3,,19F,,,{},{},19F,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001203095,"{'07A': 98.3, '07F': 98.1, '19F-II': 36.8, '19F': 35.1, '19F-I': 35.0}",1,98.3,,7F/7A,,,{},{},7F/7A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170565,"{'06B-I': 99.0, '06A-III': 96.9, '06B-II': 89.8, '06A': 89.7, '06A-V': 87.9}",1,99.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(100.0)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001122525,"{'05': 95.2, '36': 20.2, '12A': 19.7, '46': 19.6, '45': 19.4}",1,95.2,,5,,,{},{},5,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001207805,"{'19F-I': 95.6, '19F': 95.3, '19F-III': 93.8, '19F-II': 92.5, '19F-IV': 88.5}",1,95.6,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000174875,"{'19F-I': 96.0, '19F': 95.7, '19F-III': 94.1, '19F-II': 92.9, '19F-IV': 88.9}",1,96.0,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901239245,"{'14': 91.5, '36': 28.9, '09L': 25.5, '09N': 24.5, '15B': 24.2}",1,91.5,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170975,"{'06A-I': 99.5, '06B': 94.1, '06A-V': 88.4, '06A': 86.5, '06A-III': 85.1}",1,99.5,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(93.88)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001114285,"{'06C-I': 100.0, '06C': 99.8, '06D': 84.6, '06A-II': 79.6, '06A-VI': 79.6}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[2]],"{'wciN': ['b', np.float64(91.3)]}",{'wciN': 'b'},6C/6D,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000762725,"{'25F': 6.9, '25A': 6.7, '45': 6.5, '01': 5.3, '38': 4.9}",2,6.9,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001125865,"{'19F-I': 95.6, '19F': 95.3, '19F-III': 93.8, '19F-II': 92.5, '19F-IV': 88.5}",1,95.6,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170245,"{'14': 93.4, '36': 29.4, '09L': 25.4, '15B': 24.3, '15C': 24.2}",1,93.4,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170785,"{'03': 94.9, '36': 17.0, '01': 16.7, '20': 15.6, '09N': 15.3}",1,94.9,,3,,,{},{},3,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000983055,"{'36': 12.5, '20': 8.0, '06A-IV': 7.2, '45': 6.7, '01': 6.4}",1,12.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900191065,"{'01': 5.7, '20': 5.3, '25F': 4.5, '25A': 4.4, '38': 3.6}",1,5.7,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_002866355,"{'45': 6.5, '01': 6.3, '25F': 5.8, '25A': 5.6, '22F': 5.3}",3,6.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001113165,"{'36': 11.4, '20': 7.9, '23B1': 7.4, '45': 6.0, '06B-I': 5.3}",1,11.4,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001679515,"{'01': 99.0, '19F': 32.3, '19F-I': 31.8, '19F-III': 31.6, '19F-II': 31.3}",1,99.0,,1,,,{},{},1,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001172265,"{'06E': 100.0, '06B-III': 97.4, '06B-I': 44.7, '06A-III': 44.2, '06B-II': 43.6}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001719965,"{'19F-I': 97.9, '19F': 97.2, '19F-III': 96.7, '19F-II': 95.2, '19F-IV': 90.3}",1,97.9,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001163545,"{'19F-I': 95.7, '19F': 95.4, '19F-III': 93.9, '19F-II': 92.6, '19F-IV': 88.6}",1,95.7,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170885,"{'11D': 99.8, '11A': 97.0, '11F': 42.0, '11C': 35.9, '11B': 34.4}",1,99.8,,11A/11D,,,{},{},11A/11D,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900053285,"{'18C': 88.4, '18B': 88.3, '18F': 77.7, '18A': 61.2, '16F': 37.6}",1,88.4,,18C/18B,,,{},{},18C/18B,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_012911265,"{'35B': 94.0, '34': 33.3, '33F': 33.0, '35C': 32.8, '35A': 32.4}",1,94.0,,35B/35D,,,{},{},35B/35D,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_018253875,"{'03': 94.8, '01': 17.4, '36': 17.1, '20': 15.9, '09N': 15.8}",1,94.8,,3,,,{},{},3,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001348315,"{'01': 3.3, '38': 3.3, '45': 3.3, '25F': 2.9, '22F': 2.7}",1,3.3,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001112405,"{'14': 89.9, '19F-II': 22.2, '09L': 22.1, '36': 22.1, '15B': 21.4}",1,89.9,,14,,,{},{},14,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000203775,"{'06C': 88.2, '06C-I': 88.2, '06D': 86.8, '06B': 77.7, '06A-I': 77.6}",1,88.2,6A_6B_6C_6D,6A_6B_6C_6D,,[[2]],"{'wciN': ['b', np.float64(94.1)]}",{'wciN': 'b'},6C/6D,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907168765,"{'14': 92.9, '36': 27.1, '09L': 24.7, '09N': 24.5, '15B': 24.3}",1,92.9,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001143865,"{'01': 5.5, '20': 5.2, '45': 5.0, '22F': 4.7, '25F': 4.4}",1,5.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007786835,"{'01': 7.0, '45': 6.4, '25F': 5.7, '25A': 5.5, '22F': 5.2}",5,7.0,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001172305,"{'19F-I': 95.7, '19F': 95.4, '19F-III': 93.8, '19F-II': 92.6, '19F-IV': 88.6}",1,95.7,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901258975,"{'03': 97.4, '19F-I': 53.6, '19F': 53.3, '19F-III': 53.3, '19F-II': 50.6}",1,97.4,,3,,,{},{},3,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001140245,"{'06E': 100.0, '06B-III': 94.3, '06A-I': 42.6, '06B': 42.2, '06B-I': 41.8}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007787585,"{'01': 7.3, '23B1': 6.7, '45': 6.6, '22F': 5.9, '25F': 5.7}",3,7.3,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001132665,"{'22F': 4.9, '25F': 3.7, '25A': 3.6, '01': 3.2, '36': 3.0}",1,4.9,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001338155,"{'23F': 93.9, '23A': 63.4, '28A': 48.5, '23B': 47.0, '06A-III': 46.4}",1,93.9,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001167425,"{'15C': 87.7, '15B': 87.6, '15A': 64.5, '15F': 49.9, '23A': 30.2}",1,87.7,,15B/15C,,,{},{},15B/15C,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007787625,"{'10A': 100.0, '10B': 66.8, '10C': 27.5, '10F': 17.9, '22F': 14.6}",1,100.0,,10A,,,{},{},10A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170235,"{'06B-I': 99.3, '06A-III': 97.1, '06B-II': 89.7, '06A': 89.6, '06A-V': 87.8}",1,99.3,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(100.0)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001171385,"{'23F': 94.0, '23A': 63.5, '28A': 48.5, '23B': 47.0, '06A-III': 46.4}",1,94.0,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007784765,"{'45': 6.5, '01': 6.2, '25F': 5.8, '25A': 5.6, '22F': 5.2}",2,6.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007787275,"{'45': 6.5, '01': 6.0, '25F': 5.8, '25A': 5.6, '22F': 5.3}",2,6.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_003933585,"{'35A': 90.1, '35C': 85.9, '42': 85.2, '33A': 45.8, '33F': 45.3}",1,90.1,,35A/35C/42,,,{},{},35A/35C/42,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007786775,"{'01': 6.6, '25F': 5.7, '25A': 5.5, '36': 5.5, '23B1': 5.0}",1,6.6,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_009720855,"{'10A': 99.9, '10B': 66.7, '03': 34.6, '15A': 31.2, '10C': 29.1}",1,99.9,,10A,,,{},{},10A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001334075,"{'20': 4.1, '22F': 4.0, '45': 2.9, '36': 2.8, '06C-I': 2.8}",1,4.1,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001143825,"{'06C': 85.1, '06C-I': 85.1, '06D': 84.3, '06A': 76.5, '06A-IV': 72.9}",1,85.1,6A_6B_6C_6D,6A_6B_6C_6D,,[[0]],{'wciN': ['b: 83.5']},{'wciN': 0},6A_6B_6C_6D,RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001113185,"{'06E': 100.0, '06B-III': 99.4, '06B-I': 47.0, '06A-III': 46.5, '06A-II': 45.5}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170155,"{'35B': 99.4, '33F': 33.6, '35C': 33.3, '34': 33.1, '35A': 32.9}",1,99.4,,35B/35D,,,{},{},35B/35D,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007786925,"{'01': 7.3, '45': 6.4, '25F': 5.7, '25A': 5.5, '22F': 5.2}",4,7.3,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_019446115,"{'09N': 99.9, '09L': 89.0, '09A': 32.7, '09V': 32.7, '36': 30.7}",1,99.9,,9N/9L,,,{},{},9N/9L,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_008039075,"{'01': 6.8, '25F': 5.8, '36': 5.7, '25A': 5.6, '22F': 4.9}",3,6.8,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907167465,"{'14': 89.7, '36': 25.6, '15B': 24.0, '15C': 23.9, '19F-II': 22.9}",1,89.7,,14,,,{},{},14,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170345,"{'14': 92.7, '36': 27.1, '09L': 24.9, '15B': 24.2, '09N': 24.1}",1,92.7,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001117585,"{'36': 9.3, '20': 6.9, '25F': 4.5, '25A': 4.4, '45': 3.8}",1,9.3,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000385795,"{'22F': 90.1, '22A': 73.9, '06A-IV': 43.6, '06A-II': 43.2, '06A-VI': 43.1}",1,90.1,,22F,,,{},{},22F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001404235,"{'01': 6.7, '45': 5.8, '25F': 5.7, '25A': 5.5, '22F': 5.1}",2,6.7,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901217465,"{'06A-II': 94.8, '06A-VI': 94.8, '06B-II': 88.8, '06A-V': 88.4, '06A-III': 87.7}",1,94.8,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(93.22)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001151705,"{'19F-I': 95.7, '19F': 95.4, '19F-III': 93.9, '19F-II': 92.6, '19F-IV': 88.6}",1,95.7,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007785335,"{'45': 6.5, '25F': 5.8, '25A': 5.6, '22F': 5.3, '01': 5.2}",3,6.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170645,"{'22F': 97.9, '22A': 73.4, '06A': 42.6, '06B': 42.1, '06A-II': 41.9}",1,97.9,,22F,,,{},{},22F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007785275,"{'01': 6.8, '25F': 5.7, '45': 5.7, '25A': 5.5, '20': 5.3}",2,6.8,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001336275,"{'34': 70.0, '35B': 26.1, '33F2': 26.0, '33F': 22.0, '33C': 21.3}",1,70.0,,34,,,{},{},34,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001141845,"{'36': 10.5, '20': 6.8, '06A-IV': 6.4, '23B1': 5.5, '06B-I': 5.3}",1,10.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_003934065,"{'35B': 76.6, '33F': 32.9, '34': 32.9, '35C': 32.7, '35A': 32.3}",1,76.6,,35B/35D,,,{},{},35B/35D,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001141385,"{'19F-I': 96.0, '19F': 95.7, '19F-III': 94.1, '19F-II': 92.9, '19F-IV': 88.9}",1,96.0,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000762545,"{'20': 5.0, '45': 4.3, '25A': 4.1, '25F': 4.1, '01': 4.0}",1,5.0,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170175,"{'23F': 96.9, '23A': 63.8, '23B': 47.9, '28A': 47.6, '28F': 45.9}",1,96.9,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001165265,"{'20': 85.9, '36': 27.3, '13': 25.6, '09L': 25.2, '47F': 24.6}",1,85.9,,20,,,{},{},20,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001326435,"{'19F': 98.6, '19F-I': 98.5, '19F-III': 98.5, '19F-II': 94.4, '19F-IV': 89.5}",1,98.6,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_009721285,"{'15C': 88.8, '15B': 88.7, '15A': 71.7, '15F': 62.9, '19F': 48.4}",1,88.8,,15B/15C,,,{},{},15B/15C,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_003933615,"{'23B': 74.7, '23B1': 49.1, '23F': 38.3, '06A-IV': 33.7, '23A': 33.0}",1,74.7,,23B,,,{},{},23B,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001096025,"{'06C': 84.7, '06C-I': 84.7, '06D': 83.7, '06A': 76.3, '06A-IV': 72.8}",1,84.7,6A_6B_6C_6D,6A_6B_6C_6D,,[[0]],{'wciN': ['b: 83.5']},{'wciN': 0},6A_6B_6C_6D,RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901302755,"{'06A-III': 94.6, '06B-I': 93.2, '06A': 90.3, '06A-IV': 89.3, '06B-II': 89.2}",1,94.6,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(100.0)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000947295,"{'36': 11.5, '20': 8.8, '23B1': 7.4, '06A-IV': 7.1, '06B-I': 5.9}",1,11.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007787005,"{'01': 7.1, '25F': 5.6, '25A': 5.4, '22F': 5.0, '38': 4.6}",3,7.1,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001099805,"{'19F-I': 94.2, '19F': 93.9, '19F-III': 92.4, '19F-II': 91.5, '19F-IV': 87.5}",1,94.2,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001202775,"{'15C': 87.7, '15B': 87.6, '15A': 64.5, '15F': 49.9, '23A': 30.2}",1,87.7,,15B/15C,,,{},{},15B/15C,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000762525,"{'20': 4.9, '01': 4.5, '25F': 4.2, '25A': 4.1, '45': 4.1}",1,4.9,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007786585,"{'01': 7.0, '45': 5.9, '25F': 5.7, '20': 5.5, '25A': 5.5}",4,7.0,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171165,"{'06A-III': 99.5, '06B-I': 97.9, '06A': 90.9, '06B-II': 90.9, '06A-V': 90.0}",1,99.5,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(100.0)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901302595,"{'03': 97.8, '20': 18.1, '01': 16.4, '09N': 15.4, '09L': 15.1}",1,97.8,,3,,,{},{},3,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171155,"{'06A-II': 99.7, '06A-VI': 99.7, '06B-II': 91.5, '06A-V': 90.7, '06A-III': 89.3}",1,99.7,6A_6B_6C_6D,6A_6B_6C_6D,,[[0]],{'wciN': ['a: 89.84']},{'wciN': 0},6A_6B_6C_6D,RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907167975,"{'09A': 99.0, '09V': 98.8, '09N': 36.3, '09L': 34.6, '11F': 26.6}",1,99.0,,9A/9V,,,{},{},9A/9V,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170625,"{'01': 6.6, '45': 5.6, '25F': 5.4, '20': 5.2, '25A': 5.2}",2,6.6,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007786975,"{'45': 6.5, '25F': 5.8, '25A': 5.6, '22F': 5.1, '38': 4.9}",2,6.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001086105,"{'19F-I': 95.8, '19F': 95.5, '19F-III': 93.9, '19F-II': 92.7, '19F-IV': 88.7}",1,95.8,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001330015,"{'06E': 88.8, '06B-III': 84.6, '06A-I': 39.5, '06B': 39.3, '06B-I': 39.0}",1,88.8,6A_6B_6C_6D,6A_6B_6C_6D,,[[0]],{'wciN': ['g: 87.54']},{'wciN': 0},6A_6B_6C_6D,RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001105685,"{'36': 11.4, '06A-IV': 7.5, '20': 7.2, '06C': 6.1, '06B-I': 6.1}",1,11.4,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001162705,"{'25F': 5.6, '01': 5.5, '25A': 5.4, '22F': 4.9, '38': 4.5}",2,5.6,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001581795,"{'12F': 94.1, '44': 91.5, '12B': 91.3, '12A': 82.9, '46': 79.8}",1,94.1,12F_12A_12B_44_46,12F_12A_12B_44_46,,[[5]],"{'wciI': [2, np.float64(94.56)]}",{'wciI': 2},12F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001121365,"{'20': 5.0, '22F': 5.0, '25F': 5.0, '25A': 4.9, '45': 4.9}",1,5.0,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001329155,"{'19F-I': 96.0, '19F': 95.7, '19F-III': 94.1, '19F-II': 92.9, '19F-IV': 88.9}",2,96.0,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001340955,"{'15C': 87.7, '15B': 87.6, '15A': 64.5, '15F': 49.9, '23A': 30.2}",1,87.7,,15B/15C,,,{},{},15B/15C,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171325,"{'06B-II': 98.8, '06A-V': 94.7, '06A': 94.4, '06A-IV': 91.2, '06A-II': 91.0}",1,98.8,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(100.0)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_020038055,"{'11D': 50.5, '11A': 49.0, '15C': 33.1, '15B': 33.0, '11F': 28.2}",1,50.5,,"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",,,{},{},"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001719705,"{'06B-I': 94.6, '06A-III': 92.2, '06B-II': 85.6, '06A': 85.1, '06A-V': 83.7}",1,94.6,6A_6B_6C_6D,6A_6B_6C_6D,,[[0]],{'wciN': ['a: 83.39']},{'wciN': 0},6A_6B_6C_6D,RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_010604185,"{'23B': 99.5, '23B1': 64.6, '23F': 45.9, '23A': 40.4, '06A-IV': 36.6}",1,99.5,,23B,,,{},{},23B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001136725,"{'15C': 82.6, '15B': 82.5, '15A': 59.4, '15F': 45.3, '14': 27.8}",1,82.6,,15B/15C,,,{},{},15B/15C,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001084225,"{'14': 78.9, '36': 23.1, '09L': 21.7, '15B': 21.1, '15C': 21.0}",1,78.9,,14,,,{},{},14,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001330895,"{'19F-I': 86.4, '19F': 86.2, '19F-III': 84.9, '19F-II': 83.6, '19F-IV': 79.5}",1,86.4,,19F,,,{},{},19F,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001126505,"{'06E': 100.0, '06B-III': 96.2, '06B-I': 43.6, '06A-III': 43.1, '06A-I': 42.6}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901250705,"{'05': 95.0, '45': 22.3, '36': 21.4, '20': 20.1, '12A': 19.8}",1,95.0,,5,,,{},{},5,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001345675,"{'01': 6.5, '36': 6.5, '06A-IV': 6.3, '20': 6.1, '38': 4.8}",1,6.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001925155,"{'06E': 83.0, '06B-III': 76.2, '23B1': 38.8, '19A-II': 33.5, '19AF': 32.3}",1,83.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001581545,"{'01': 7.0, '45': 6.4, '25F': 5.6, '25A': 5.4, '22F': 5.1}",3,7.0,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171675,"{'19F-I': 99.7, '19F': 96.7, '19F-III': 96.7, '19F-II': 93.9, '19F-IV': 89.3}",1,99.7,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001336955,"{'23F': 94.0, '23A': 63.5, '28A': 48.5, '23B': 47.0, '06A-III': 46.3}",1,94.0,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001163645,"{'25F': 5.5, '25A': 5.4, '45': 4.6, '36': 4.1, '01': 3.1}",1,5.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007785005,"{'01': 5.7, '23B1': 5.1, '36': 5.0, '38': 4.8, '45': 4.7}",1,5.7,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001329955,"{'06E': 99.7, '06B-III': 94.6, '06A-I': 42.6, '06B': 42.2, '06B-I': 42.2}",1,99.7,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171415,"{'10A': 100.0, '10B': 66.8, '10C': 27.5, '10F': 17.9, '22F': 15.3}",1,100.0,,10A,,,{},{},10A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007784815,"{'45': 6.4, '25F': 5.8, '25A': 5.6, '38': 4.9, '01': 4.6}",2,6.4,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007786695,"{'01': 7.1, '45': 5.9, '25F': 5.7, '20': 5.5, '25A': 5.5}",3,7.1,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001581395,"{'01': 27.2, '06C': 20.9, '06C-I': 20.9, '06A-II': 20.0, '06A-V': 20.0}",1,27.2,,"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",,,{},{},"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171105,"{'16F': 96.7, '19F-IV': 44.8, '19F-II': 44.0, '19F': 43.0, '19F-I': 42.4}",1,96.7,,16F,,,{},{},16F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_002866305,"{'01': 6.7, '45': 5.8, '25F': 5.7, '20': 5.5, '25A': 5.5}",3,6.7,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001087645,"{'06E': 100.0, '06B-III': 95.7, '06B-I': 43.1, '06A-I': 42.6, '06A-III': 42.6}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007785565,"{'19A-I': 98.2, '19A-II': 96.6, '19A': 86.8, '19A-III': 86.6, '19AF': 61.1}",1,98.2,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(95.25)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001115725,"{'22F': 4.9, '25F': 3.9, '25A': 3.8, '45': 3.5, '01': 3.2}",1,4.9,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001119545,"{'19F-I': 95.8, '19F': 95.5, '19F-III': 93.9, '19F-II': 92.7, '19F-IV': 88.7}",1,95.8,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907169265,"{'09A': 99.4, '09V': 99.2, '09N': 36.0, '09L': 34.5, '11F': 26.6}",1,99.4,,9A/9V,,,{},{},9A/9V,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007787515,"{'01': 7.4, '45': 6.4, '25F': 5.9, '25A': 5.7, '22F': 5.4}",3,7.4,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001165185,"{'15C': 87.7, '15B': 87.6, '15A': 64.5, '15F': 49.9, '23A': 30.2}",1,87.7,,15B/15C,,,{},{},15B/15C,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001092565,"{'34': 93.3, '33F2': 35.3, '35B': 31.2, '33F': 29.3, '33C': 28.8}",1,93.3,,34,,,{},{},34,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000203755,"{'06C-I': 99.7, '06C': 99.5, '06D': 84.6, '06A-II': 79.4, '06A-VI': 79.4}",1,99.7,6A_6B_6C_6D,6A_6B_6C_6D,,[[2]],"{'wciN': ['b', np.float64(91.3)]}",{'wciN': 'b'},6C/6D,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001909215,"{'03': 95.2, '36': 17.0, '20': 15.3, '09L': 13.6, '14': 13.6}",1,95.2,,3,,,{},{},3,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001139985,"{'19F-I': 95.5, '19F': 95.2, '19F-III': 93.7, '19F-II': 92.4, '19F-IV': 88.4}",1,95.5,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001156425,"{'14': 94.5, '36': 24.8, '15B': 24.2, '15C': 24.1, '09L': 23.6}",1,94.5,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170215,"{'06E': 100.0, '06B-III': 99.5, '06B-I': 46.8, '06A-III': 46.3, '06A-II': 45.3}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_002866145,"{'45': 6.5, '25F': 5.7, '01': 5.6, '25A': 5.5, '22F': 5.2}",2,6.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_002358015,"{'03': 95.2, '36': 17.4, '01': 16.8, '20': 15.9, '09N': 15.8}",1,95.2,,3,,,{},{},3,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007784895,"{'38': 95.2, '25F': 81.2, '25A': 80.3, '36': 11.8, '20': 8.1}",1,95.2,25F_25A_38,25F_25A_38,,"[[9], [19]]","{'wcyD': ['b', np.float64(100.0)], 'wcyV': np.float64(100.0)}","{'wcyD': 'b', 'wcyV': 'detected'}",38,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001092005,"{'19F-I': 95.7, '19F': 95.4, '19F-III': 93.9, '19F-II': 92.6, '19F-IV': 88.6}",1,95.7,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900193095,"{'38': 97.6, '25F': 83.0, '25A': 82.1, '36': 11.2, '20': 7.6}",1,97.6,25F_25A_38,25F_25A_38,,"[[9], [19]]","{'wcyD': ['b', np.float64(100.0)], 'wcyV': np.float64(100.0)}","{'wcyD': 'b', 'wcyV': 'detected'}",38,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907171745,"{'14': 87.3, '36': 28.4, '09L': 24.8, '09N': 23.8, '15B': 23.4}",1,87.3,,14,,,{},{},14,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001105045,"{'06E': 99.8, '06B-III': 95.4, '06B-I': 42.9, '06A-I': 42.6, '06A-III': 42.4}",1,99.8,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001336295,"{'06E': 88.3, '06B-III': 88.2, '06B-I': 42.5, '06A-III': 42.0, '06A-V': 41.2}",1,88.3,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001196495,"{'22A': 94.2, '22F': 75.3, '06A-IV': 45.5, '06A-II': 43.8, '06B-I': 43.8}",1,94.2,,22A,,,{},{},22A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907170085,"{'14': 90.1, '36': 27.9, '09L': 24.3, '15B': 24.2, '15C': 24.1}",1,90.1,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001145685,"{'06E': 100.0, '06B-III': 97.1, '06B-I': 44.4, '06A-III': 43.9, '06B-II': 43.3}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_002866325,"{'36': 7.4, '45': 6.4, '01': 5.9, '22F': 5.9, '38': 4.6}",1,7.4,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001148425,"{'10A': 99.3, '10B': 67.0, '10C': 27.7, '10F': 18.1, '06B-I': 15.2}",1,99.3,,10A,,,{},{},10A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001150485,"{'23F': 93.0, '23A': 63.3, '06A-IV': 53.2, '06B-II': 51.8, '23B': 50.9}",1,93.0,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001329975,"{'06E': 100.0, '06B-III': 98.4, '06B-I': 46.0, '06A-III': 45.5, '06A-II': 44.5}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001135065,"{'38': 98.8, '25F': 84.0, '25A': 83.1, '36': 11.7, '20': 8.2}",1,98.8,25F_25A_38,25F_25A_38,,"[[9], [19]]","{'wcyD': ['b', np.float64(100.0)], 'wcyV': np.float64(100.0)}","{'wcyD': 'b', 'wcyV': 'detected'}",38,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_012911225,"{'35B': 88.8, '34': 33.3, '33F': 33.0, '35C': 32.9, '35A': 32.5}",1,88.8,,35B/35D,,,{},{},35B/35D,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170545,"{'19F': 100.0, '19F-III': 97.5, '19F-I': 96.8, '19F-II': 95.3, '19F-IV': 90.4}",1,100.0,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001136345,"{'35B': 99.7, '33F': 33.7, '35C': 33.5, '34': 33.3, '35A': 33.1}",1,99.7,,35B/35D,,,{},{},35B/35D,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001329935,"{'06E': 98.1, '06B-III': 97.2, '06B-I': 46.6, '06A-III': 46.1, '06A-II': 45.1}",1,98.1,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001091985,"{'19A': 100.0, '19A-III': 99.8, '19A-I': 86.2, '19A-II': 83.7, '19AF': 57.2}",1,100.0,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(100.0)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001209905,"{'05': 95.2, '45': 20.0, '12A': 19.7, '46': 19.6, '04': 19.3}",1,95.2,,5,,,{},{},5,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170615,"{'23F': 99.3, '23A': 65.1, '28A': 47.8, '23B': 47.7, '06A-V': 45.5}",1,99.3,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001132625,"{'20': 5.4, '22F': 4.9, '25F': 3.9, '25A': 3.8, '06C-I': 3.5}",1,5.4,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170325,"{'19A': 88.8, '19A-III': 88.6, '19A-II': 81.9, '19A-I': 80.3, '19AF': 55.3}",1,88.8,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(97.62)]}",{'wzy': 1},19A,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001107365,"{'06E': 100.0, '06B-III': 98.1, '06B-I': 45.7, '06A-III': 45.2, '06A-II': 44.2}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001112745,"{'04': 98.2, '45': 31.9, '12F': 23.8, '44': 23.6, '12A': 22.7}",1,98.2,,4,,,{},{},4,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001199295,"{'38': 88.1, '25F': 84.3, '25A': 83.5, '36': 11.4, '20': 7.6}",1,88.1,25F_25A_38,25F_25A_38,,"[[0], [18]]","{'wcyD': ['b: 22.59'], 'wcyV': np.float64(4.69)}","{'wcyD': 0, 'wcyV': 'not_detected'}",25F_25A_38,RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001164905,"{'38': 88.1, '25F': 84.4, '25A': 83.5, '36': 11.8, '20': 7.8}",1,88.1,25F_25A_38,25F_25A_38,,"[[0], [18]]","{'wcyD': ['b: 22.59'], 'wcyV': np.float64(4.69)}","{'wcyD': 0, 'wcyV': 'not_detected'}",25F_25A_38,RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001164725,"{'38': 87.3, '25F': 83.7, '25A': 82.9, '36': 10.7, '20': 6.7}",1,87.3,25F_25A_38,25F_25A_38,,"[[0], [18]]","{'wcyD': ['b: 22.59'], 'wcyV': np.float64(4.69)}","{'wcyD': 0, 'wcyV': 'not_detected'}",25F_25A_38,RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001195745,"{'36': 8.2, '06A-IV': 4.6, '20': 3.7, '06B-I': 3.3, '22F': 3.2}",1,8.2,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001335135,"{'19B': 95.7, '19C': 70.0, '19F-II': 53.9, '19F-I': 53.1, '19F': 53.0}",1,95.7,,19B,,,{},{},19B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001581615,"{'36': 10.3, '23B1': 6.8, '45': 6.3, '06A-IV': 6.1, '20': 5.9}",1,10.3,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001715905,"{'33F': 72.1, '33A': 69.0, '33F2': 52.8, '35B': 36.9, '35C': 36.1}",1,72.1,,33F/33A,,,{},{},33F/33A,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_003934445,"{'15C': 73.3, '15B': 73.2, '15A': 50.5, '15F': 40.4, '23A': 32.2}",1,73.3,,15B/15C,,,{},{},15B/15C,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007787655,"{'01': 7.3, '45': 6.5, '25F': 5.8, '25A': 5.6, '22F': 5.4}",3,7.3,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907167385,"{'14': 93.1, '36': 27.2, '09L': 25.1, '15B': 24.3, '15C': 24.2}",1,93.1,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171525,"{'06D': 87.2, '06C': 85.2, '06C-I': 85.2, '06A-I': 76.0, '06B': 75.9}",1,87.2,6A_6B_6C_6D,6A_6B_6C_6D,,[[0]],{'wciN': ['b: 89.8']},{'wciN': 0},6A_6B_6C_6D,RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001338715,"{'35B': 89.9, '34': 33.4, '33F': 32.8, '35C': 31.9, '35A': 31.6}",1,89.9,,35B/35D,,,{},{},35B/35D,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171335,"{'06A-II': 99.8, '06A-VI': 99.8, '06B-II': 91.8, '06A-V': 91.1, '06A-III': 89.6}",1,99.8,6A_6B_6C_6D,6A_6B_6C_6D,,[[0]],{'wciN': ['a: 89.84']},{'wciN': 0},6A_6B_6C_6D,RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_009721185,"{'38': 98.1, '25F': 83.7, '25A': 82.8, '23A': 31.4, '23B': 26.5}",1,98.1,25F_25A_38,25F_25A_38,,"[[9], [19]]","{'wcyD': ['b', np.float64(100.0)], 'wcyV': np.float64(100.0)}","{'wcyD': 'b', 'wcyV': 'detected'}",38,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001087925,"{'20': 5.2, '36': 5.0, '45': 4.7, '25A': 4.2, '25F': 4.2}",1,5.2,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001124245,"{'06A-III': 99.8, '06B-I': 98.2, '06B-II': 91.1, '06A': 90.8, '06A-V': 90.2}",1,99.8,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(100.0)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901218555,"{'23B': 82.4, '23B1': 62.5, '23F': 31.7, '28A': 28.6, '06B-III': 27.9}",1,82.4,,23B,,,{},{},23B,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170225,"{'23A': 99.7, '23F': 67.3, '23B': 43.6, '19F-II': 37.9, '15B': 37.2}",1,99.7,,23A,,,{},{},23A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_012911085,"{'35B': 75.0, '33F': 33.3, '34': 33.3, '35C': 33.2, '35A': 32.8}",1,75.0,,35B/35D,,,{},{},35B/35D,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001170045,"{'19F-I': 95.7, '19F': 95.4, '19F-III': 93.9, '19F-II': 92.6, '19F-IV': 88.6}",1,95.7,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001141665,"{'14': 90.2, '36': 29.6, '09L': 24.4, '09N': 23.5, '19F-II': 22.2}",1,90.2,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_019446135,"{'15B': 99.8, '15C': 99.6, '15A': 62.7, '15F': 48.3, '23A': 32.9}",1,99.8,,15B/15C,,,{},{},15B/15C,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001123925,"{'06E': 100.0, '06B-III': 99.6, '06B-I': 47.0, '06A-III': 46.5, '06A-II': 45.5}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000334795,"{'01': 99.3, '19F': 32.0, '19F-I': 31.5, '19F-III': 31.3, '19F-II': 31.0}",1,99.3,,1,,,{},{},1,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901237415,"{'03': 97.4, '01': 17.5, '20': 15.5, '09N': 15.3, '09L': 15.1}",1,97.4,,3,,,{},{},3,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_002889015,"{'35F': 87.7, '47F': 64.5, '35B': 25.2, '34': 25.0, '29': 24.5}",1,87.7,,35F,,,{},{},35F,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901247715,"{'19F-I': 97.9, '19F': 97.2, '19F-III': 96.7, '19F-II': 95.2, '19F-IV': 90.3}",1,97.9,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001093905,"{'11C': 100.0, '11B': 91.1, '11A': 33.7, '11D': 33.4, '23B1': 20.1}",1,100.0,,11B/11C,,,{},{},11B/11C,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901254495,"{'23F': 92.4, '23A': 61.1, '28A': 48.1, '23B': 46.6, '06A-IV': 46.6}",1,92.4,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001132125,"{'46': 98.1, '12A': 95.9, '12B': 84.2, '44': 82.2, '12F': 81.9}",1,98.1,12F_12A_12B_44_46,12F_12A_12B_44_46,,[[4]],"{'wciI': [1, np.float64(100.0)]}",{'wciI': 1},12A/12B/44/46,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001138765,"{'23F': 91.9, '23A': 62.2, '28A': 48.1, '23B': 46.9, '06A-III': 46.4}",1,91.9,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001334475,"{'11F': 61.7, '11D': 38.3, '11A': 36.8, '09A': 25.3, '09V': 25.3}",1,61.7,,"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",,,{},{},"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001343235,"{'10B': 96.2, '10A': 64.5, '10F': 18.9, '10C': 18.5, '22F': 12.3}",1,96.2,,10B,,,{},{},10B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_002866405,"{'01': 6.6, '45': 5.8, '25F': 5.7, '20': 5.5, '25A': 5.5}",3,6.6,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000334715,"{'01': 99.3, '19F': 32.3, '19F-I': 31.8, '19F-III': 31.6, '19F-II': 31.3}",1,99.3,,1,,,{},{},1,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001162965,{1: 0.3},1,0.3,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001171445,"{'19F-I': 90.1, '19F': 89.8, '19F-III': 88.7, '19F-II': 87.0, '19F-IV': 83.0}",1,90.1,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901243065,"{'03': 97.4, '01': 16.8, '20': 15.4, '09N': 15.3, '09L': 14.9}",1,97.4,,3,,,{},{},3,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907170065,"{'14': 92.7, '36': 28.4, '09L': 24.6, '15B': 24.2, '15C': 24.1}",1,92.7,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170705,"{'17F': 95.1, '06B': 45.7, '06B-I': 45.3, '06A-I': 45.2, '06A-III': 45.2}",1,95.1,,17F,,,{},{},17F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170985,"{'23F': 97.8, '23A': 63.3, '28A': 48.3, '23B': 48.2, '06A-IV': 46.8}",1,97.8,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001121065,"{'22F': 4.9, '25A': 4.3, '25F': 4.3, '45': 4.2, '38': 3.4}",1,4.9,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001207355,"{'25F': 6.2, '25A': 6.0, '01': 5.1, '22F': 4.8, '38': 4.4}",1,6.2,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001106105,"{'23F': 94.0, '23A': 63.5, '28A': 48.5, '23B': 47.0, '06A-III': 46.3}",1,94.0,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907166895,"{'09A': 13.0, '09V': 13.0, '22F': 6.0, '06B-I': 6.0, '35B': 5.8}",1,13.0,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001330755,"{'19F-I': 95.8, '19F': 95.5, '19F-III': 93.9, '19F-II': 92.7, '19F-IV': 88.7}",1,95.8,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001194385,"{'35B': 94.8, '33F': 33.9, '35C': 33.6, '35A': 33.2, '34': 33.1}",1,94.8,,35B/35D,,,{},{},35B/35D,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007787475,"{'45': 6.5, '25F': 5.8, '25A': 5.6, '01': 5.3, '22F': 5.2}",2,6.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901240095,"{'06A-V': 98.8, '06B-II': 93.9, '06A': 91.4, '06A-II': 89.5, '06A-VI': 89.5}",1,98.8,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(96.61)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001123105,"{'36': 10.1, '06A-IV': 6.4, '20': 5.2, '23B1': 5.2, '06B-I': 5.1}",1,10.1,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007786805,"{'01': 7.2, '45': 6.4, '25F': 5.9, '25A': 5.7, '22F': 5.2}",4,7.2,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170855,"{'14': 99.3, '09L': 26.8, '36': 25.8, '09N': 24.0, '15B': 23.9}",1,99.3,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001403815,"{'20': 86.5, '36': 27.7, '13': 25.6, '47F': 24.6, '09L': 24.0}",1,86.5,,20,,,{},{},20,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171505,"{'14': 99.9, '09L': 26.3, '36': 26.1, '09N': 24.3, '15B': 24.3}",1,99.9,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001156845,{1: 0.1},1,0.1,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001164305,"{'36': 7.4, '20': 6.9, '06C': 4.4, '06C-I': 4.4, '25F': 4.3}",1,7.4,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001121265,"{'13': 98.9, '09L': 28.1, '20': 28.0, '09N': 27.9, '14': 26.8}",1,98.9,,13,,,{},{},13,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001720025,"{'14': 88.6, '36': 26.3, '09L': 25.6, '09N': 24.7, '15B': 24.3}",1,88.6,,14,,,{},{},14,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007787285,"{'01': 6.7, '45': 5.9, '25F': 5.7, '20': 5.5, '25A': 5.5}",3,6.7,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001097385,"{'19F-I': 92.7, '19F': 92.4, '19F-III': 90.9, '19F-II': 90.1, '19F-IV': 86.1}",1,92.7,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171395,"{'23F': 97.6, '23A': 63.1, '23B': 48.2, '28A': 48.1, '06A-IV': 46.6}",1,97.6,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001159805,"{'06E': 97.8, '06B-III': 94.0, '06B-I': 43.5, '06A-III': 43.0, '06A-I': 42.5}",1,97.8,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001728875,"{'06B-III': 79.0, '06E': 76.9, '06B-I': 40.7, '06A-III': 40.4, '06A-II': 40.0}",1,79.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[0]],{'wciN': ['g: 41.42']},{'wciN': 0},6A_6B_6C_6D,RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001581695,"{'45': 6.4, '25F': 5.7, '25A': 5.5, '22F': 5.3, '01': 4.9}",3,6.4,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001720095,"{'19F-I': 95.4, '19F': 95.1, '19F-III': 94.2, '19F-II': 92.8, '19F-IV': 87.8}",1,95.4,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001337895,"{'06E': 100.0, '06B-III': 99.4, '06B-I': 47.0, '06A-III': 46.5, '06A-II': 45.5}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001735995,"{'06A-II': 58.1, '06A-VI': 58.0, '06A-III': 56.3, '06B-I': 56.3, '06A-V': 55.2}",1,58.1,,"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",,,{},{},"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001719695,"{'14': 87.0, '19F-IV': 25.7, '36': 25.4, '09L': 24.6, '09N': 24.3}",1,87.0,,14,,,{},{},14,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001157965,"{'19F-I': 95.6, '19F': 95.3, '19F-III': 93.8, '19F-II': 92.5, '19F-IV': 88.5}",1,95.6,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001087225,"{'36': 12.2, '06A-IV': 8.5, '20': 7.3, '06B-I': 7.3, '06C': 7.2}",1,12.2,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907172155,"{'14': 92.5, '36': 28.1, '09L': 24.4, '15B': 24.2, '15C': 24.1}",1,92.5,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_003970445,"{'15B': 61.9, '15C': 61.7, '15A': 39.1, '23A': 33.4, '15F': 30.6}",1,61.9,,"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",,,{},{},"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001728845,"{'19A-I': 99.4, '19A-II': 97.4, '19A': 88.0, '19A-III': 87.8, '19AF': 62.0}",1,99.4,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(95.25)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901246585,"{'06C-I': 88.6, '06C': 88.5, '06D': 84.5, '06B-I': 76.9, '06A-III': 76.6}",1,88.6,6A_6B_6C_6D,6A_6B_6C_6D,,[[0]],{'wciN': ['b: 83.5']},{'wciN': 0},6A_6B_6C_6D,RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901239585,"{'06A-II': 80.7, '06A-VI': 80.7, '06A-III': 80.6, '06A-V': 79.5, '06B-I': 79.4}",1,80.7,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(93.22)]}",{'wciN': 'a'},6A/6B,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_008039115,"{'45': 5.8, '25F': 5.7, '01': 5.6, '20': 5.5, '25A': 5.5}",3,5.8,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001870545,"{'19F-I': 96.0, '19F': 95.7, '19F-III': 94.1, '19F-II': 92.9, '19F-IV': 88.9}",1,96.0,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_002866245,"{'45': 6.1, '01': 6.0, '25F': 5.8, '20': 5.7, '25A': 5.6}",2,6.1,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007786765,"{'45': 5.9, '25F': 5.7, '20': 5.5, '25A': 5.5, '22F': 5.4}",3,5.9,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_008039135,"{'01': 6.8, '45': 5.9, '25F': 5.7, '20': 5.5, '25A': 5.5}",3,6.8,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170675,"{'34': 99.3, '33F2': 35.4, '35B': 33.3, '33F': 30.0, '33C': 28.7}",1,99.3,,34,,,{},{},34,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_003933685,"{'35A': 91.2, '35C': 87.0, '42': 86.3, '33A': 46.4, '33F': 45.9}",1,91.2,,35A/35C/42,,,{},{},35A/35C/42,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001330335,"{'19F-I': 95.1, '19F': 94.9, '19F-III': 93.4, '19F-II': 92.0, '19F-IV': 88.0}",1,95.1,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001102425,"{'23F': 94.0, '23A': 63.5, '28A': 48.5, '23B': 47.0, '06A-III': 46.4}",1,94.0,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001720075,"{'06A-II': 83.0, '06A-VI': 82.9, '06A-III': 82.8, '06A-V': 81.8, '06B-I': 81.5}",1,83.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(90.6)]}",{'wciN': 'a'},6A/6B,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007785315,"{'45': 6.5, '01': 5.9, '25F': 5.8, '25A': 5.6, '22F': 5.1}",2,6.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001089005,"{'06E': 99.7, '06B-III': 99.1, '06B-I': 46.7, '06A-III': 46.2, '06A-II': 45.2}",1,99.7,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001584885,"{'12F': 97.0, '44': 93.7, '12B': 93.0, '12A': 80.7, '46': 77.6}",1,97.0,12F_12A_12B_44_46,12F_12A_12B_44_46,,[[5]],"{'wciI': [2, np.float64(100.0)]}",{'wciI': 2},12F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171635,"{'06B-II': 99.8, '06A-V': 95.7, '06A': 94.4, '06A-IV': 92.1, '06A-II': 91.9}",1,99.8,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(100.0)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001133965,"{'06E': 76.8, '06B-III': 75.9, '06D': 65.8, '06B-I': 63.7, '06A-III': 63.4}",1,76.8,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_009721195,"{'35B': 99.3, '23F': 58.1, '23A': 56.3, '15A': 44.7, '15F': 44.1}",1,99.3,,35B/35D,,,{},{},35B/35D,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170665,"{'23F': 99.4, '23A': 65.2, '28A': 47.8, '23B': 47.7, '06A-V': 45.6}",1,99.4,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171025,"{'35F': 99.7, '47F': 74.5, '34': 26.7, '35B': 26.3, '29': 22.5}",1,99.7,,35F,,,{},{},35F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_010604145,"{'34': 93.0, '33F2': 34.6, '35B': 30.9, '33F': 28.9, '33C': 27.9}",1,93.0,,34,,,{},{},34,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170055,"{'19F-I': 92.2, '19F-III': 89.8, '19F': 89.2, '19F-II': 86.6, '19F-IV': 84.7}",1,92.2,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001336795,"{'36': 11.2, '23B1': 7.1, '06A-IV': 6.6, '20': 5.7, '06C': 5.2}",1,11.2,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_002246925,"{'15C': 92.1, '15B': 92.0, '15A': 57.7, '15F': 44.7, '23A': 34.7}",1,92.1,,15B/15C,,,{},{},15B/15C,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001301035,"{'35B': 100.0, '33F': 33.7, '35C': 33.5, '34': 33.3, '35A': 33.1}",1,100.0,,35B/35D,,,{},{},35B/35D,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001111025,"{'36': 12.8, '20': 8.2, '06A-IV': 8.1, '06C': 7.3, '06C-I': 7.3}",1,12.8,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001122065,"{'06A': 88.6, '06A-III': 88.2, '06B-I': 87.0, '06B-II': 86.7, '06A-II': 86.3}",1,88.6,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(94.64)]}",{'wciN': 'a'},6A/6B,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_019446245,"{'03': 83.9, '36': 16.3, '20': 15.3, '01': 15.1, '09N': 14.7}",1,83.9,,3,,,{},{},3,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907171535,"{'14': 92.6, '36': 28.2, '09L': 24.8, '15B': 24.2, '15C': 24.1}",1,92.6,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001154725,"{'36': 10.8, '06A-IV': 6.9, '20': 6.8, '06C': 5.4, '06B-I': 5.3}",1,10.8,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001163085,"{'06E': 100.0, '06B-III': 97.5, '06B-I': 44.8, '06A-III': 44.3, '06B-II': 43.7}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000334835,"{'01': 99.1, '19F': 32.3, '19F-I': 31.8, '19F-III': 31.6, '19F-II': 31.3}",1,99.1,,1,,,{},{},1,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171375,"{'13': 98.8, '20': 29.3, '09L': 28.4, '09N': 27.9, '36': 27.5}",1,98.8,,13,,,{},{},13,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001169405,"{'19F-I': 95.6, '19F': 95.3, '19F-III': 93.8, '19F-II': 92.5, '19F-IV': 88.5}",1,95.6,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170955,"{'35F': 99.3, '47F': 74.6, '34': 26.7, '35B': 26.4, '29': 22.5}",1,99.3,,35F,,,{},{},35F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001112365,"{'01': 4.9, '22F': 4.9, '25F': 4.8, '25A': 4.7, '38': 3.9}",2,4.9,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001337715,"{'19F': 94.7, '19F-I': 94.2, '19F-III': 93.1, '19F-II': 91.8, '19F-IV': 88.1}",1,94.7,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170515,"{'10A': 100.0, '10B': 66.8, '10C': 27.5, '10F': 17.9, '22F': 14.2}",1,100.0,,10A,,,{},{},10A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900193265,"{'06C-I': 98.8, '06C': 98.6, '06D': 84.4, '06A-II': 78.5, '06A-VI': 78.5}",1,98.8,6A_6B_6C_6D,6A_6B_6C_6D,,[[2]],"{'wciN': ['b', np.float64(91.3)]}",{'wciN': 'b'},6C/6D,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000939355,"{'10A': 99.3, '10B': 67.0, '10C': 27.7, '10F': 18.1, '06B-I': 15.2}",1,99.3,,10A,,,{},{},10A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001719755,"{'22F': 95.8, '22A': 73.4, '06A': 42.6, '06A-II': 42.3, '06A-VI': 42.2}",1,95.8,,22F,,,{},{},22F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001338775,"{'17F': 99.7, '06B': 44.4, '06B-I': 43.8, '06A-III': 43.7, '06D': 43.6}",1,99.7,,17F,,,{},{},17F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171585,"{'21': 100.0, '22F': 35.5, '06A-IV': 32.8, '06A-II': 32.1, '06A-VI': 32.0}",1,100.0,,21,,,{},{},21,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_019446645,"{'45': 5.7, '25F': 5.6, '01': 5.4, '25A': 5.4, '20': 4.9}",1,5.7,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001137925,"{'10B': 99.5, '10A': 65.3, '10F': 20.1, '10C': 18.8, '47A': 12.6}",1,99.5,,10B,,,{},{},10B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907170175,"{'14': 92.6, '36': 27.7, '15B': 24.2, '15C': 24.1, '09L': 23.9}",1,92.6,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001200795,"{'13': 95.3, '36': 31.6, '09L': 28.2, '09N': 26.8, '14': 26.1}",1,95.3,,13,,,{},{},13,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000203735,"{'06C-I': 99.9, '06C': 99.7, '06D': 84.6, '06A-II': 79.6, '06A-VI': 79.6}",1,99.9,6A_6B_6C_6D,6A_6B_6C_6D,,[[2]],"{'wciN': ['b', np.float64(91.3)]}",{'wciN': 'b'},6C/6D,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001209105,"{'23F': 94.0, '23A': 63.5, '28A': 48.5, '23B': 47.0, '06A-III': 46.4}",1,94.0,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001104265,"{'06E': 100.0, '06B-III': 94.2, '06A-I': 42.6, '06B': 42.2, '06B-I': 41.6}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001138265,"{'14': 94.6, '36': 26.2, '15B': 24.2, '15C': 24.1, '09L': 24.0}",1,94.6,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907166865,"{'09A': 84.7, '09V': 84.5, '09N': 27.7, '09L': 26.9, '11F': 26.6}",1,84.7,,9A/9V,,,{},{},9A/9V,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001124145,"{'06E': 99.5, '06B-III': 98.3, '06B-I': 46.4, '06A-III': 45.9, '06A-II': 45.0}",1,99.5,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907170255,"{'14': 89.7, '36': 25.7, '09L': 22.7, '09N': 22.0, '15B': 22.0}",1,89.7,,14,,,{},{},14,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001169165,"{'22F': 5.0, '25F': 4.5, '25A': 4.4, '01': 3.7, '38': 3.6}",2,5.0,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007784875,"{'01': 6.8, '45': 6.3, '25F': 5.6, '25A': 5.4, '22F': 5.0}",4,6.8,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001117445,"{'23F': 94.5, '23A': 63.5, '06A-IV': 53.2, '06B-II': 51.6, '23B': 50.8}",1,94.5,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001103125,"{'06E': 99.7, '06B-III': 94.6, '06A-I': 42.6, '06B-I': 42.4, '06B': 42.2}",1,99.7,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001106325,"{'06E': 100.0, '06B-III': 99.3, '06B-I': 46.7, '06A-III': 46.2, '06A-II': 45.2}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001164945,"{'19F-I': 95.8, '19F': 95.5, '19F-III': 94.0, '19F-II': 92.7, '19F-IV': 88.7}",1,95.8,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001155345,"{'36': 10.6, '06A-IV': 6.5, '23B1': 5.6, '20': 5.5, '06B-I': 5.3}",1,10.6,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001139345,"{'10B': 78.0, '10A': 61.4, '10F': 18.6, '10C': 16.4, '35B': 12.1}",1,78.0,,10B,,,{},{},10B,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_012911165,"{'35B': 59.7, '34': 33.0, '33F': 32.9, '35C': 32.7, '35A': 32.3}",1,59.7,,"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",,,{},{},"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001104485,"{'06E': 100.0, '06B-III': 93.2, '06A-I': 42.6, '06B': 42.2, '06B-I': 40.8}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901224095,"{'06A-II': 91.4, '06A-VI': 91.4, '06A-V': 90.1, '06A-III': 89.7, '06B-II': 89.7}",1,91.4,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(93.22)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907167365,"{'14': 93.4, '36': 27.2, '09L': 24.3, '15B': 24.3, '15C': 24.2}",1,93.4,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001115225,"{'37': 98.8, '33F': 77.0, '33A': 75.7, '33F2': 70.4, '35B': 30.1}",1,98.8,,37,,,{},{},37,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001167145,"{'19A-I': 99.3, '19A-II': 97.7, '19A': 87.9, '19A-III': 87.7, '19AF': 62.0}",1,99.3,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(95.25)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900034435,"{'19F-I': 99.8, '19F': 96.8, '19F-III': 96.8, '19F-II': 94.0, '19F-IV': 89.4}",1,99.8,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171275,"{'23B': 99.4, '23B1': 64.6, '23F': 45.6, '23A': 39.8, '06A-IV': 36.6}",1,99.4,,23B,,,{},{},23B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907169015,"{'09A': 99.7, '09V': 99.5, '09N': 36.7, '09L': 35.2, '11F': 26.6}",1,99.7,,9A/9V,,,{},{},9A/9V,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001334995,"{'01': 6.3, '20': 5.0, '45': 4.9, '22F': 4.8, '25F': 4.8}",1,6.3,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001173585,"{'01': 96.9, '19F': 32.3, '19F-I': 31.8, '19F-III': 31.6, '19F-II': 31.3}",1,96.9,,1,,,{},{},1,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001581165,"{'45': 6.2, '25F': 5.6, '25A': 5.5, '22F': 4.9, '38': 4.7}",2,6.2,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_019446155,"{'11D': 99.9, '11A': 97.1, '11F': 42.0, '11C': 35.8, '11B': 34.3}",1,99.9,,11A/11D,,,{},{},11A/11D,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901236265,"{'16F': 69.8, '28F': 42.7, '28A': 40.2, '18F': 33.7, '18A': 32.9}",1,69.8,,"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",,,{},{},"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001553495,"{'06E': 99.9, '06B-III': 99.5, '06B-I': 47.1, '06A-III': 46.6, '06A-II': 45.6}",1,99.9,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001142065,"{'06A': 77.6, '06B-II': 76.9, '06A-III': 76.3, '06A-V': 76.2, '06A-VI': 76.2}",1,77.6,6A_6B_6C_6D,6A_6B_6C_6D,,[[0]],{'wciN': ['a: 13.88']},{'wciN': 0},6A_6B_6C_6D,RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001581805,"{'01': 6.6, '45': 6.3, '25F': 5.6, '25A': 5.4, '22F': 5.2}",3,6.6,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001860725,"{'22F': 98.6, '22A': 73.1, '06A-IV': 43.8, '06A': 42.9, '06B': 42.4}",1,98.6,,22F,,,{},{},22F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001340935,"{'35F': 94.1, '47F': 70.8, '34': 24.3, '35B': 21.9, '29': 19.3}",1,94.1,,35F,,,{},{},35F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171575,"{'19F-I': 94.5, '19F-III': 92.2, '19F': 92.1, '19F-II': 88.8, '19F-IV': 85.0}",1,94.5,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001330255,"{'19F-I': 95.7, '19F': 95.4, '19F-III': 93.9, '19F-II': 92.6, '19F-IV': 88.6}",1,95.7,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001336855,"{'19A-I': 91.8, '19A-II': 90.1, '19A': 81.3, '19A-III': 81.1, '19AF': 58.0}",1,91.8,19A_19AF,19A_19AF,,[[0]],{'wzy': ['1: 59.77']},{'wzy': 0},19A_19AF,RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001129205,"{'23F': 96.8, '23A': 66.4, '28A': 47.4, '06A': 46.0, '28F': 45.1}",1,96.8,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001132205,"{'06E': 100.0, '06B-III': 94.5, '06A-I': 42.6, '06B': 42.2, '06B-I': 41.9}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170125,"{'06D': 87.2, '06C': 85.2, '06C-I': 85.2, '06A-I': 76.0, '06B': 75.9}",1,87.2,6A_6B_6C_6D,6A_6B_6C_6D,,[[0]],{'wciN': ['b: 89.8']},{'wciN': 0},6A_6B_6C_6D,RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007787335,"{'01': 6.9, '45': 6.5, '25F': 5.8, '25A': 5.6, '22F': 5.3}",3,6.9,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001100445,"{'19F-I': 95.7, '19F': 95.4, '19F-III': 93.9, '19F-II': 92.6, '19F-IV': 88.6}",1,95.7,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001090025,"{'06E': 100.0, '06B-III': 93.4, '06A-I': 42.6, '06B': 42.2, '06B-I': 41.0}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170505,"{'19A-I': 99.4, '19A-II': 97.7, '19A': 88.0, '19A-III': 87.8, '19AF': 62.0}",1,99.4,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(95.25)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001108345,"{'36': 5.9, '20': 5.3, '45': 4.7, '06C-I': 4.3, '06C': 4.2}",1,5.9,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001109865,"{'37': 51.6, '36': 9.7, '20': 5.7, '23B1': 5.6, '06B-I': 4.8}",1,51.6,,"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",,,{},{},"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007787155,"{'45': 5.8, '25F': 5.7, '20': 5.5, '25A': 5.5, '01': 5.3}",2,5.8,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001163325,"{'15C': 95.4, '15B': 95.3, '15A': 60.8, '15F': 47.2, '23A': 34.4}",1,95.4,,15B/15C,,,{},{},15B/15C,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901218215,"{'06E': 99.6, '06B-III': 98.3, '06B-I': 45.9, '06A-III': 45.4, '06A-II': 44.6}",1,99.6,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170905,"{'19A-I': 99.4, '19A-II': 97.2, '19A': 87.4, '19A-III': 87.2, '19AF': 61.8}",1,99.4,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(92.87)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171085,"{'14': 99.7, '09L': 26.1, '36': 26.1, '09N': 24.3, '15B': 24.3}",1,99.7,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007786685,"{'01': 7.0, '45': 5.4, '22F': 4.6, '12A': 4.4, '46': 4.4}",4,7.0,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001160645,"{'19A': 99.3, '19A-III': 99.1, '19A-I': 86.2, '19A-II': 83.9, '19AF': 57.2}",1,99.3,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(100.0)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001340295,"{'06E': 100.0, '06B-III': 97.6, '06B-I': 44.9, '06A-III': 44.4, '06B-II': 43.8}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007786965,"{'01': 6.7, '45': 5.9, '25F': 5.7, '20': 5.5, '25A': 5.5}",2,6.7,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007787245,"{'01': 6.3, '45': 6.1, '25F': 5.8, '25A': 5.6, '22F': 5.2}",3,6.3,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901250495,"{'19A-I': 99.4, '19A-II': 97.7, '19A': 88.0, '19A-III': 87.8, '19AF': 62.0}",1,99.4,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(95.25)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001334495,"{'33B': 89.8, '33D': 89.7, '35B': 33.6, '33F2': 30.0, '35C': 26.2}",1,89.8,,"Mixed serotypes- {'33B', '33D'}",,,{},{},"Mixed serotypes- {'33B', '33D'}",AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001117525,"{'14': 92.9, '36': 25.2, '15B': 23.5, '15C': 23.4, '09L': 22.5}",1,92.9,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170745,"{'09A': 99.7, '09V': 99.5, '09N': 38.3, '09L': 36.7, '11F': 26.6}",1,99.7,,9A/9V,,,{},{},9A/9V,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001301375,"{'15A': 98.6, '15F': 73.8, '15C': 62.1, '15B': 62.0, '23F': 31.9}",1,98.6,15F_15A,15F_15A,,"[[11], [13], [15], [17]]","{'glf': 0, 'rmlB': 0, 'rmlD': 0, 'wcjE': 0}","{'glf': 'not_detected', 'rmlB': 'not_detected', 'rmlD': 'not_detected', 'wcjE': 'not_detected'}",15A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001100725,"{'19F-I': 67.6, '19F': 66.8, '19F-III': 66.2, '19F-II': 64.2, '19F-IV': 60.1}",1,67.6,,"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",,,{},{},"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901241775,"{'06B-III': 96.2, '06E': 96.1, '06B-I': 48.3, '06A-III': 47.8, '06A-II': 47.1}",1,96.2,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001169765,"{'23A': 96.6, '23F': 67.7, '23B': 45.9, '19F-II': 39.4, '15B': 38.5}",1,96.6,,23A,,,{},{},23A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001909855,"{'03': 95.2, '36': 16.9, '20': 15.2, '14': 13.6, '09L': 13.2}",1,95.2,,3,,,{},{},3,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001139585,"{'19F-I': 96.0, '19F': 95.7, '19F-III': 94.1, '19F-II': 92.9, '19F-IV': 88.9}",1,96.0,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170845,"{'23F': 98.9, '23A': 64.7, '28A': 47.5, '23B': 47.4, '06A-V': 45.6}",1,98.9,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001338975,"{'19F-I': 95.6, '19F': 95.3, '19F-III': 93.8, '19F-II': 92.5, '19F-IV': 88.5}",1,95.6,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170385,"{'09N': 99.7, '09L': 88.7, '09A': 32.8, '09V': 32.8, '36': 32.4}",1,99.7,,9N/9L,,,{},{},9N/9L,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907170365,"{'14': 92.2, '36': 25.8, '09L': 24.3, '15B': 24.3, '15C': 24.2}",1,92.2,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907167755,"{'14': 93.4, '36': 27.1, '15B': 24.3, '15C': 24.2, '09L': 23.7}",1,93.4,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001104185,"{'06A': 90.4, '06A-III': 89.3, '06A-II': 89.2, '06A-VI': 89.2, '06B-II': 89.2}",1,90.4,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(93.22)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_008039035,"{'01': 6.3, '45': 5.9, '25F': 5.7, '25A': 5.5, '22F': 5.1}",3,6.3,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001088045,"{'15C': 87.7, '15B': 87.6, '15A': 64.5, '15F': 49.9, '23A': 30.2}",1,87.7,,15B/15C,,,{},{},15B/15C,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001092605,"{'23F': 94.0, '23A': 63.5, '28A': 48.5, '23B': 47.0, '06A-III': 46.3}",1,94.0,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001336695,"{'36': 6.4, '20': 6.3, '45': 6.2, '38': 5.1, '25F': 4.8}",1,6.4,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171225,"{'19F-II': 99.6, '19F': 95.4, '19F-III': 94.4, '19F-I': 94.1, '19F-IV': 93.3}",1,99.6,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001099625,"{'19F-I': 95.8, '19F': 95.5, '19F-III': 93.9, '19F-II': 92.7, '19F-IV': 88.7}",1,95.8,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001099605,"{'09L': 96.7, '09N': 88.1, '36': 31.5, '09A': 31.4, '09V': 31.4}",1,96.7,,9N/9L,,,{},{},9N/9L,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000334675,"{'01': 99.4, '19F': 32.3, '19F-I': 31.8, '19F-III': 31.6, '19F-II': 31.3}",1,99.4,,1,,,{},{},1,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001115305,"{'06B-III': 88.6, '06E': 88.3, '06B-I': 42.5, '06A-III': 41.6, '06A-IV': 41.3}",1,88.6,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001101065,"{'10B': 99.5, '10A': 65.3, '10F': 20.1, '10C': 18.8, '47A': 12.6}",1,99.5,,10B,,,{},{},10B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170305,"{'06A-II': 97.9, '06A-VI': 97.9, '06B-II': 90.4, '06A-V': 89.6, '06A-III': 89.2}",1,97.9,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(93.22)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001111345,"{'06E': 100.0, '06B-III': 96.2, '06B-I': 43.6, '06A-III': 43.1, '06A-I': 42.6}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007787545,"{'25F': 5.7, '01': 5.6, '20': 5.5, '25A': 5.5, '45': 5.5}",4,5.7,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901250425,"{'01': 6.8, '45': 6.5, '38': 4.7, '12A': 4.5, '25F': 4.5}",3,6.8,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000174855,"{'19A': 99.3, '19A-III': 99.1, '19A-I': 86.2, '19A-II': 83.9, '19AF': 57.2}",1,99.3,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(100.0)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907167135,"{'09A': 99.6, '09V': 99.4, '09N': 37.0, '09L': 35.6, '11F': 26.6}",1,99.6,,9A/9V,,,{},{},9A/9V,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001147485,"{'19F-I': 95.8, '19F': 95.5, '19F-III': 93.9, '19F-II': 92.7, '19F-IV': 88.7}",1,95.8,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001143725,"{'36': 9.4, '20': 5.8, '23B1': 5.7, '06B-I': 5.5, '06C': 5.4}",1,9.4,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001072305,"{'11D': 100.0, '11A': 97.2, '11F': 42.0, '11C': 35.9, '11B': 34.4}",1,100.0,,11A/11D,,,{},{},11A/11D,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171425,"{'19F-I': 99.7, '19F': 96.7, '19F-III': 96.7, '19F-II': 93.9, '19F-IV': 89.3}",1,99.7,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_003933535,"{'23B': 72.9, '23B1': 46.9, '23F': 38.2, '06A-IV': 33.7, '23A': 32.9}",1,72.9,,23B,,,{},{},23B,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900025875,"{'10A': 100.0, '10B': 66.8, '10C': 27.5, '10F': 17.9, '22F': 15.4}",1,100.0,,10A,,,{},{},10A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001330915,"{'19F-I': 93.4, '19F': 93.1, '19F-III': 91.6, '19F-II': 90.3, '19F-IV': 86.3}",1,93.4,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007787355,"{'01': 7.6, '45': 6.3, '25F': 5.7, '25A': 5.5, '22F': 5.0}",4,7.6,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001211445,"{'34': 93.2, '33F2': 35.3, '35B': 31.9, '33F': 29.3, '33C': 28.8}",1,93.2,,34,,,{},{},34,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007785415,"{'45': 6.1, '01': 6.0, '25F': 5.7, '25A': 5.6, '38': 4.6}",2,6.1,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907169215,"{'14': 92.8, '36': 26.9, '09L': 24.8, '15B': 24.3, '15C': 24.2}",1,92.8,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001149185,"{'06E': 100.0, '06B-III': 95.3, '06A-I': 42.6, '06B-I': 42.6, '06B': 42.2}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001095665,"{'45': 6.6, '01': 6.2, '25F': 5.5, '25A': 5.3, '22F': 4.6}",3,6.6,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001581635,"{'45': 6.5, '25F': 5.8, '25A': 5.6, '01': 5.4, '22F': 5.3}",3,6.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001581665,"{'01': 6.8, '45': 6.4, '25F': 5.7, '25A': 5.5, '22F': 5.2}",4,6.8,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_923172295,"{'45': 2.8, '22F': 2.6, '35B': 2.2, '09L': 1.9, '38': 1.9}",1,2.8,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001152625,"{'15C': 96.2, '15B': 96.1, '15A': 67.4, '15F': 60.0, '23A': 46.7}",1,96.2,,15B/15C,,,{},{},15B/15C,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001130745,"{'36': 9.4, '23B1': 5.7, '20': 5.6, '06B-I': 5.5, '06C': 5.4}",1,9.4,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_002866425,"{'01': 7.0, '45': 5.9, '25F': 5.7, '20': 5.5, '25A': 5.5}",3,7.0,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001168545,"{'19F-I': 95.9, '19F': 95.6, '19F-III': 94.0, '19F-II': 92.8, '19F-IV': 88.8}",1,95.9,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901241935,"{'06A-II': 91.7, '06A-VI': 91.7, '06B-II': 89.0, '06A-V': 88.7, '06A-III': 87.6}",1,91.7,6A_6B_6C_6D,6A_6B_6C_6D,,[[0]],{'wciN': ['a: 84.81']},{'wciN': 0},6A_6B_6C_6D,RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_923172285,"{'45': 2.5, '22F': 1.7, '18A': 1.5, '35B': 1.5, '09L': 1.4}",1,2.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001925145,"{'06E': 99.7, '06B-III': 98.5, '06B-I': 45.7, '06A-III': 45.5, '06A-II': 44.5}",1,99.7,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001335895,"{'15C': 87.7, '15B': 87.6, '15A': 64.5, '15F': 49.9, '23A': 30.2}",1,87.7,,15B/15C,,,{},{},15B/15C,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007786715,"{'01': 6.1, '45': 5.9, '25F': 5.7, '20': 5.5, '25A': 5.5}",2,6.1,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001089265,"{'14': 98.9, '36': 25.9, '09L': 24.9, '09N': 24.0, '15B': 23.9}",1,98.9,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007787445,"{'45': 6.3, '25F': 5.5, '22F': 5.4, '25A': 5.3, '01': 4.6}",2,6.3,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001719685,"{'19F-II': 94.9, '19F': 90.7, '19F-III': 89.8, '19F-I': 89.5, '19F-IV': 88.6}",1,94.9,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170135,"{'19F-I': 95.5, '19F': 95.2, '19F-III': 93.6, '19F-II': 92.4, '19F-IV': 88.6}",1,95.5,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001129925,"{'20': 81.7, '13': 25.6, '36': 25.1, '47F': 24.6, '09L': 24.4}",1,81.7,,20,,,{},{},20,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007787185,"{'25F': 7.5, '25A': 7.3, '01': 6.4, '45': 6.3, '22F': 5.3}",3,7.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901240795,"{'08': 99.6, '06A-II': 24.7, '06A-VI': 24.6, '02': 24.4, '06B-II': 24.1}",1,99.6,,8,,,{},{},8,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001910135,"{'03': 95.2, '36': 17.3, '20': 15.7, '01': 15.5, '09N': 15.4}",1,95.2,,3,,,{},{},3,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_020140495,"{'35B': 99.6, '33F': 33.3, '35C': 33.2, '34': 32.9, '35A': 32.8}",1,99.6,,35B/35D,,,{},{},35B/35D,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001089085,"{'35A': 99.9, '35C': 85.2, '42': 84.6, '33A': 42.9, '33F': 42.6}",1,99.9,,35A/35C/42,,,{},{},35A/35C/42,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001120705,"{'19F-I': 96.0, '19F': 95.7, '19F-III': 94.1, '19F-II': 92.9, '19F-IV': 88.9}",1,96.0,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901252415,"{'18C': 88.5, '18B': 88.4, '18F': 77.8, '18A': 61.6, '16F': 37.6}",1,88.5,,18C/18B,,,{},{},18C/18B,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170895,"{'19F-II': 99.2, '19F': 95.0, '19F-III': 94.1, '19F-I': 93.7, '19F-IV': 92.9}",1,99.2,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001336935,"{'03': 95.1, '01': 17.6, '20': 15.2, '09N': 15.1, '09L': 15.0}",1,95.1,,3,,,{},{},3,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001111505,"{'19F-I': 95.6, '19F': 95.3, '19F-III': 93.8, '19F-II': 92.5, '19F-IV': 88.5}",1,95.6,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_012911235,"{'35B': 81.9, '33F': 32.9, '34': 32.8, '35C': 32.7, '35A': 32.3}",1,81.9,,35B/35D,,,{},{},35B/35D,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_002265125,"{'23F': 81.1, '23A': 50.9, '23B': 45.4, '06A-IV': 44.5, '06B-II': 44.5}",1,81.1,,23F,,,{},{},23F,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001094505,"{'19A': 99.3, '19A-III': 99.1, '19A-I': 86.2, '19A-II': 83.9, '19AF': 57.2}",1,99.3,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(100.0)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001146005,"{'36': 10.7, '20': 7.6, '06A-IV': 7.3, '45': 6.3, '06B-I': 6.0}",1,10.7,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171475,"{'14': 99.8, '09L': 26.7, '36': 26.1, '09N': 24.3, '15B': 24.2}",1,99.8,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001150665,"{'06E': 99.8, '06B-III': 94.2, '06A-I': 42.5, '06B': 42.1, '06B-I': 41.6}",1,99.8,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(96.61)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_009720925,"{'23B': 99.3, '23B1': 64.5, '23F': 46.5, '15A': 46.2, '23A': 45.9}",1,99.3,,23B,,,{},{},23B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001715955,"{'19A-I': 99.4, '19A-II': 97.7, '19A': 88.0, '19A-III': 87.8, '19AF': 62.0}",1,99.4,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(95.25)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001137025,"{'01': 5.8, '25F': 5.6, '25A': 5.4, '22F': 4.9, '38': 4.6}",1,5.8,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001151105,"{'22F': 5.1, '20': 5.0, '01': 4.8, '45': 4.7, '25F': 4.4}",2,5.1,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171515,"{'09A': 99.5, '09V': 99.3, '09N': 38.1, '09L': 36.4, '11F': 26.6}",1,99.5,,9A/9V,,,{},{},9A/9V,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900030755,"{'07A': 99.7, '07F': 99.5, '19F-II': 36.4, '19F-IV': 35.8, '19F': 34.9}",1,99.7,,7F/7A,,,{},{},7F/7A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_002866165,"{'01': 6.5, '45': 6.2, '20': 5.7, '25F': 5.7, '25A': 5.5}",3,6.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001170085,"{'19F-I': 95.8, '19F': 95.5, '19F-III': 94.0, '19F-II': 92.7, '19F-IV': 88.7}",1,95.8,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170085,"{'11A': 99.2, '11D': 96.8, '11F': 40.1, '11C': 36.2, '11B': 34.8}",1,99.2,,11A/11D,,,{},{},11A/11D,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001088785,"{'22A': 94.2, '22F': 75.4, '06A-IV': 45.8, '06A-II': 44.1, '06B-I': 44.1}",1,94.2,,22A,,,{},{},22A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001117205,"{'34': 92.9, '33F2': 34.6, '35B': 30.1, '33F': 29.0, '33C': 28.0}",1,92.9,,34,,,{},{},34,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007787045,"{'45': 6.5, '01': 5.9, '25F': 5.7, '25A': 5.5, '22F': 5.2}",4,6.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001104665,"{'14': 99.8, '09L': 26.7, '36': 25.9, '09N': 24.7, '15B': 24.1}",1,99.8,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001097645,"{'19F-I': 96.0, '19F': 95.7, '19F-III': 94.1, '19F-II': 92.9, '19F-IV': 88.9}",1,96.0,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171605,"{'21': 95.7, '22F': 38.1, '06A-II': 34.5, '06A-VI': 34.4, '06A-III': 33.9}",1,95.7,,21,,,{},{},21,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_012911405,"{'35B': 77.0, '34': 31.8, '33F': 31.4, '35C': 31.4, '35A': 31.2}",1,77.0,,35B/35D,,,{},{},35B/35D,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_012911745,"{'14': 66.4, '36': 25.4, '09L': 23.9, '09N': 23.2, '20': 21.5}",1,66.4,,"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",,,{},{},"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001326355,"{'07A': 99.6, '07F': 99.5, '19F-II': 36.4, '19F-IV': 35.8, '19F': 34.9}",1,99.6,,7F/7A,,,{},{},7F/7A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001147605,"{'20': 5.0, '22F': 4.8, '45': 4.3, '25A': 4.0, '25F': 4.0}",1,5.0,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001159065,"{'06E': 99.9, '06B-III': 97.4, '06B-I': 44.9, '06A-III': 44.4, '06A-IV': 43.6}",1,99.9,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(96.61)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007787665,"{'01': 7.3, '45': 6.5, '25F': 5.8, '25A': 5.6, '22F': 5.4}",3,7.3,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001167525,"{'06A': 89.7, '06A-III': 89.3, '06B-I': 88.0, '06B-II': 87.8, '06A-II': 87.3}",1,89.7,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(100.0)]}",{'wciN': 'a'},6A/6B,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001109805,"{'19F-I': 94.1, '19F': 93.8, '19F-III': 92.2, '19F-II': 91.0, '19F-IV': 87.1}",1,94.1,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007785155,"{'01': 6.9, '25F': 5.7, '25A': 5.5, '20': 5.2, '22F': 5.2}",3,6.9,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007785025,"{'06A-II': 93.2, '06A-VI': 93.1, '06B-II': 87.0, '06A-V': 86.6, '06A-III': 86.0}",1,93.2,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(93.22)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170595,"{'19F-I': 99.8, '19F': 96.8, '19F-III': 96.8, '19F-II': 94.0, '19F-IV': 89.4}",1,99.8,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_009721085,"{'23A': 61.6, '23F': 58.6, '28A': 57.9, '28F': 56.2, '01': 42.0}",1,61.6,,"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",,,{},{},"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900189385,"{'14': 99.6, '36': 26.1, '09L': 24.4, '15B': 24.3, '15C': 24.2}",1,99.6,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001585505,"{'12F': 96.2, '44': 93.1, '12B': 92.8, '12A': 84.9, '46': 81.8}",1,96.2,12F_12A_12B_44_46,12F_12A_12B_44_46,,[[5]],"{'wciI': [2, np.float64(94.56)]}",{'wciI': 2},12F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001340835,"{'23F': 48.9, '23A': 29.9, '28A': 21.7, '28F': 20.9, '23B': 20.6}",1,48.9,,"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",,,{},{},"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_019446725,"{'45': 5.9, '25F': 5.1, '25A': 4.9, '38': 4.2, '22F': 4.1}",2,5.9,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000385695,"{'19F-I': 95.8, '19F': 95.5, '19F-III': 93.9, '19F-II': 92.7, '19F-IV': 88.7}",1,95.8,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001157985,"{'45': 6.3, '01': 5.8, '25F': 4.9, '25A': 4.7, '22F': 4.1}",2,6.3,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000385675,"{'06E': 98.8, '06B-III': 96.6, '06B-I': 44.7, '06A-III': 44.4, '06A-IV': 43.6}",1,98.8,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900055335,"{'34': 93.6, '33F2': 35.4, '35B': 33.0, '33F': 29.8, '33C': 28.8}",1,93.6,,34,,,{},{},34,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171265,"{'06B-II': 98.6, '06A-V': 94.5, '06A': 94.4, '06A-IV': 91.0, '06A-II': 90.8}",1,98.6,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(100.0)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007787525,"{'36': 10.7, '23B1': 6.8, '06A-IV': 6.6, '45': 6.2, '20': 6.0}",1,10.7,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001336315,"{'15C': 73.7, '15B': 73.6, '15A': 48.3, '15F': 37.4, '23A': 23.4}",1,73.7,,15B/15C,,,{},{},15B/15C,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001161445,"{'23A': 99.5, '23F': 67.3, '23B': 43.6, '19F-II': 37.8, '15B': 37.1}",1,99.5,,23A,,,{},{},23A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000334815,"{'01': 99.2, '19F': 32.0, '19F-I': 31.5, '19F-III': 31.3, '19F-II': 31.0}",1,99.2,,1,,,{},{},1,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001150965,"{'19F-I': 96.0, '19F': 95.7, '19F-III': 94.1, '19F-II': 92.9, '19F-IV': 88.9}",1,96.0,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001581145,"{'08': 99.5, '06A-II': 24.4, '06A-VI': 24.3, '02': 24.1, '06B-II': 23.8}",1,99.5,,8,,,{},{},8,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170775,"{'19F-I': 99.6, '19F': 96.6, '19F-III': 96.6, '19F-II': 93.8, '19F-IV': 89.4}",1,99.6,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007787295,"{'01': 95.9, '19F': 32.1, '19F-I': 31.6, '19F-III': 31.4, '19F-II': 31.1}",1,95.9,,1,,,{},{},1,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001091565,"{'19F-I': 95.9, '19F': 95.6, '19F-III': 94.0, '19F-II': 92.8, '19F-IV': 88.8}",1,95.9,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001114725,"{'36': 8.6, '20': 6.3, '25F': 4.8, '25A': 4.7, '01': 4.1}",1,8.6,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001119305,"{'25F': 5.8, '25A': 5.6, '45': 5.5, '22F': 4.8, '38': 4.7}",2,5.8,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_002249715,"{'17F': 93.4, '06A-III': 45.6, '06B-I': 45.4, '06A-IV': 45.3, '06A': 44.5}",1,93.4,,17F,,,{},{},17F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171185,"{'19F-I': 99.7, '19F': 96.7, '19F-III': 96.7, '19F-II': 93.9, '19F-IV': 89.3}",1,99.7,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001151785,"{'19F-I': 95.8, '19F': 95.5, '19F-III': 93.9, '19F-II': 92.7, '19F-IV': 88.7}",1,95.8,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001171825,"{'06A': 90.4, '06A-III': 89.2, '06A-II': 89.1, '06A-VI': 89.1, '06B-II': 89.1}",1,90.4,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(93.22)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001093425,"{'19F-I': 95.5, '19F': 95.2, '19F-III': 93.7, '19F-II': 92.4, '19F-IV': 88.4}",1,95.5,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001169585,"{'06E': 100.0, '06B-III': 99.2, '06B-I': 46.8, '06A-III': 46.3, '06A-II': 45.3}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001099025,"{'06E': 99.9, '06B-III': 95.2, '06B-I': 43.1, '06A-I': 42.6, '06A-III': 42.6}",1,99.9,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001329995,"{'19F-I': 95.7, '19F': 95.4, '19F-III': 93.9, '19F-II': 92.6, '19F-IV': 88.6}",1,95.7,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_012911185,"{'35B': 59.9, '33F': 32.0, '34': 31.6, '35C': 31.3, '35A': 30.9}",1,59.9,,"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",,,{},{},"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_019446615,"{'03': 93.6, '36': 16.9, '20': 15.8, '09N': 15.7, '09L': 15.5}",1,93.6,,3,,,{},{},3,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001161365,"{'15C': 95.8, '15B': 95.7, '15A': 61.2, '15F': 47.6, '23A': 34.7}",1,95.8,,15B/15C,,,{},{},15B/15C,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001084745,"{'38': 99.5, '25F': 84.7, '25A': 83.7, '36': 11.7, '20': 8.2}",1,99.5,25F_25A_38,25F_25A_38,,"[[9], [19]]","{'wcyD': ['b', np.float64(100.0)], 'wcyV': np.float64(100.0)}","{'wcyD': 'b', 'wcyV': 'detected'}",38,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001093105,"{'06E': 100.0, '06B-III': 95.3, '06A-I': 42.6, '06B-I': 42.6, '06B': 42.2}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001581855,"{'23F': 93.6, '24F': 83.6, '24B': 79.5, '24F2': 76.2, '23A': 73.6}",1,93.6,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001581825,"{'08': 86.3, '06A-III': 18.6, '06C': 18.3, '06A-II': 18.3, '06C-I': 18.3}",1,86.3,,8,,,{},{},8,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901254235,"{'06E': 97.7, '06B-III': 97.0, '06B-I': 46.4, '06A-III': 45.9, '06A-II': 45.1}",1,97.7,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001201095,"{'19F-I': 96.0, '19F': 95.7, '19F-III': 94.1, '19F-II': 92.9, '19F-IV': 88.9}",1,96.0,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001113885,"{'06E': 99.9, '06B-III': 95.9, '06B-I': 43.3, '06A-III': 42.8, '06A-I': 42.5}",1,99.9,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000762505,"{'01': 5.2, '20': 5.2, '25F': 4.2, '45': 4.2, '25A': 4.1}",1,5.2,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007787715,"{'01': 7.5, '45': 6.5, '25F': 5.8, '25A': 5.6, '22F': 5.2}",3,7.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_002866255,"{'01': 7.5, '45': 6.5, '25F': 5.8, '25A': 5.6, '22F': 5.2}",4,7.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001301075,"{'07A': 99.7, '07F': 99.5, '19F-II': 36.4, '19F-IV': 35.8, '19F': 34.9}",1,99.7,,7F/7A,,,{},{},7F/7A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907169415,"{'14': 92.7, '36': 28.6, '09L': 24.9, '15B': 24.2, '15C': 24.1}",1,92.7,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001127865,"{'38': 99.5, '25F': 84.7, '25A': 83.7, '36': 11.7, '20': 8.2}",1,99.5,25F_25A_38,25F_25A_38,,"[[9], [19]]","{'wcyD': ['b', np.float64(100.0)], 'wcyV': np.float64(100.0)}","{'wcyD': 'b', 'wcyV': 'detected'}",38,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001141405,"{'36': 11.6, '20': 7.5, '06A-IV': 7.5, '06C': 6.1, '06C-I': 6.1}",1,11.6,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001174525,"{'06E': 100.0, '06B-III': 99.4, '06B-I': 47.0, '06A-III': 46.5, '06A-II': 45.5}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171535,"{'19F-II': 99.3, '19F': 95.1, '19F-III': 94.1, '19F-I': 93.8, '19F-IV': 93.0}",1,99.3,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001339055,"{'20': 86.4, '36': 27.7, '13': 25.6, '09L': 24.8, '47F': 24.6}",1,86.4,,20,,,{},{},20,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001585635,"{'12F': 96.7, '44': 93.4, '12B': 92.7, '12A': 80.4, '46': 77.3}",1,96.7,12F_12A_12B_44_46,12F_12A_12B_44_46,,[[5]],"{'wciI': [2, np.float64(100.0)]}",{'wciI': 2},12F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001198395,"{'07C': 0.2, '17F': 0.2, '07B': 0.1, '40': 0.1}",1,0.2,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001149225,"{'23F': 96.8, '23A': 66.4, '28A': 47.4, '06A': 46.0, '28F': 45.1}",1,96.8,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001203335,"{'18C': 88.6, '18B': 88.5, '18F': 78.1, '18A': 59.6, '16F': 37.7}",1,88.6,,18C/18B,,,{},{},18C/18B,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171495,"{'19F-I': 99.9, '19F': 96.9, '19F-III': 96.9, '19F-II': 94.1, '19F-IV': 89.5}",1,99.9,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171075,"{'23F': 99.4, '23A': 65.2, '28A': 47.8, '23B': 47.7, '06A-V': 45.6}",1,99.4,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001336255,"{'19F-I': 87.1, '19F': 86.9, '19F-II': 85.9, '19F-III': 85.5, '19F-IV': 82.0}",1,87.1,,19F,,,{},{},19F,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001095345,"{'25F': 5.0, '22F': 4.9, '25A': 4.8, '01': 4.4, '38': 4.1}",2,5.0,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001210365,"{'06E': 100.0, '06B-III': 99.5, '06B-I': 46.9, '06A-III': 46.4, '06A-II': 45.4}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007784935,"{'01': 7.1, '45': 6.5, '25F': 5.8, '25A': 5.6, '22F': 5.3}",2,7.1,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001142105,"{'36': 5.6, '22F': 4.8, '20': 4.7, '25F': 4.7, '23B1': 4.7}",1,5.6,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900036525,"{'10A': 100.0, '10B': 66.8, '10C': 27.5, '10F': 17.9, '22F': 14.0}",1,100.0,,10A,,,{},{},10A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001120045,"{'36': 9.3, '20': 6.9, '06B-I': 5.6, '06C': 5.4, '06C-I': 5.4}",1,9.3,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170495,"{'06E': 99.9, '06B-III': 99.5, '06B-I': 46.9, '06A-III': 46.4, '06A-II': 45.4}",1,99.9,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900191395,"{'14': 98.8, '36': 25.5, '09L': 24.7, '15B': 23.8, '15C': 23.7}",1,98.8,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001137625,"{'06E': 100.0, '06B-III': 99.6, '06B-I': 47.1, '06A-III': 46.6, '06A-II': 45.6}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_009720955,"{'15C': 95.6, '15B': 95.5, '11D': 69.8, '11A': 67.3, '15A': 65.6}",1,95.6,,15B/15C,,,{},{},15B/15C,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907170145,"{'12F': 96.1, '14': 92.5, '44': 91.8, '12B': 89.5, '12A': 84.1}",1,96.1,,"Mixed serotypes- {'12F_12A_12B_44_46', '14'}",,,{},{},"Mixed serotypes- {'12F_12A_12B_44_46', '14'}",AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907168815,"{'14': 81.8, '36': 21.4, '20': 19.2, '15B': 18.8, '09L': 18.7}",1,81.8,,14,,,{},{},14,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001581585,"{'22F': 7.1, '45': 6.5, '20': 5.8, '38': 4.9, '06A-IV': 4.8}",2,7.1,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001172205,"{'19F': 95.1, '19F-I': 94.3, '19F-III': 93.5, '19F-II': 91.9, '19F-IV': 88.2}",1,95.1,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000334755,"{'01': 99.2, '19F': 32.1, '19F-I': 31.6, '19F-III': 31.4, '19F-II': 31.1}",1,99.2,,1,,,{},{},1,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001581735,"{'45': 6.4, '25F': 6.3, '25A': 6.1, '01': 4.9, '38': 4.9}",3,6.4,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900172405,"{'19F-I': 99.9, '19F': 96.9, '19F-III': 96.9, '19F-II': 94.1, '19F-IV': 89.5}",1,99.9,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901340055,"{'15C': 95.8, '15B': 95.7, '15A': 61.1, '15F': 47.5, '23A': 34.7}",1,95.8,,15B/15C,,,{},{},15B/15C,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170355,"{'23B': 99.2, '23B1': 64.4, '23F': 45.8, '23A': 40.0, '06A-IV': 36.8}",1,99.2,,23B,,,{},{},23B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001131405,"{'06A-II': 97.9, '06A-VI': 97.9, '06B-II': 90.4, '06A-V': 89.6, '06A-III': 89.2}",1,97.9,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(93.22)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001330655,"{'06E': 100.0, '06B-III': 94.5, '06A-I': 42.6, '06B': 42.2, '06B-I': 41.9}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901241505,"{'13': 93.6, '36': 31.3, '20': 29.4, '09L': 28.8, '09N': 28.3}",1,93.6,,13,,,{},{},13,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001170705,"{'06E': 100.0, '06B-III': 98.7, '06B-I': 46.1, '06A-III': 45.6, '06A-II': 44.6}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001344035,"{'28F': 98.6, '28A': 92.2, '23F': 47.6, '16F': 45.9, '06B-I': 39.4}",1,98.6,,28F/28A,,,{},{},28F/28A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007785515,"{'01': 7.2, '25F': 6.9, '25A': 6.7, '45': 6.5, '22F': 5.4}",3,7.2,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001092225,"{'36': 13.1, '20': 8.1, '06A-IV': 7.6, '06C': 6.2, '06B-I': 6.2}",3,13.1,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001581325,"{'14': 87.0, '36': 27.2, '09L': 25.2, '09N': 24.1, '15B': 23.3}",1,87.0,,14,,,{},{},14,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170465,"{'23F': 99.4, '23A': 65.2, '28A': 47.8, '23B': 47.7, '06A-V': 45.6}",1,99.4,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907166915,"{'19F-II': 99.3, '19F': 95.1, '19F-III': 94.1, '19F-I': 93.8, '19F-IV': 93.0}",1,99.3,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007785215,"{'01': 6.0, '45': 5.9, '25F': 5.7, '20': 5.5, '25A': 5.5}",3,6.0,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001697025,"{'07C': 99.5, '07B': 76.6, '40': 74.5, '29': 56.1, '24F': 49.0}",1,99.5,,7C,,,{},{},7C,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001334095,"{'20': 5.4, '45': 5.2, '22F': 5.0, '25F': 4.6, '25A': 4.5}",1,5.4,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001170065,"{'36': 11.5, '06A-IV': 7.4, '20': 6.4, '06C': 6.0, '06B-I': 6.0}",1,11.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_019446435,"{'35B': 88.8, '23B1': 73.8, '23B': 58.9, '06A-I': 31.3, '06B': 30.7}",1,88.8,,35B/35D,,,{},{},35B/35D,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001118365,"{'38': 88.0, '25F': 84.3, '25A': 83.5, '36': 11.9, '20': 7.9}",1,88.0,25F_25A_38,25F_25A_38,,"[[0], [18]]","{'wcyD': ['b: 22.59'], 'wcyV': np.float64(4.69)}","{'wcyD': 0, 'wcyV': 'not_detected'}",25F_25A_38,RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001195525,"{'19F-I': 95.6, '19F': 95.3, '19F-III': 93.8, '19F-II': 92.5, '19F-IV': 88.5}",1,95.6,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001111925,"{'06E': 91.9, '06B-III': 88.0, '06A-I': 39.2, '06A-III': 39.1, '06B-I': 38.9}",1,91.9,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170315,"{'16F': 96.8, '19F-IV': 44.8, '19F-II': 44.0, '19F': 43.0, '19F-I': 42.4}",1,96.8,,16F,,,{},{},16F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001120165,"{'19F': 73.6, '19F-I': 73.6, '19F-III': 72.1, '19F-II': 71.0, '19F-IV': 67.8}",1,73.6,,19F,,,{},{},19F,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001735975,"{'14': 88.1, '36': 26.9, '09L': 24.2, '09N': 23.0, '19F-II': 22.2}",1,88.1,,14,,,{},{},14,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001153145,"{'25F': 6.0, '45': 6.0, '25A': 5.8, '38': 4.6, '35B': 4.3}",2,6.0,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170045,"{'11D': 100.0, '11A': 97.2, '11F': 42.0, '11C': 35.9, '11B': 34.4}",1,100.0,,11A/11D,,,{},{},11A/11D,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007786845,"{'01': 7.3, '45': 6.2, '25F': 5.4, '25A': 5.2, '22F': 5.1}",5,7.3,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_009720665,"{'09N': 99.0, '09L': 88.4, '19A': 67.0, '19A-III': 66.8, '19A-II': 63.8}",1,99.0,,9N/9L,,,{},{},9N/9L,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907169125,"{'09A': 99.7, '09V': 99.5, '09N': 37.1, '09L': 35.8, '11F': 26.6}",1,99.7,,9A/9V,,,{},{},9A/9V,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_012911105,"{'35B': 81.4, '34': 33.3, '33F': 32.9, '35C': 32.8, '35A': 32.4}",1,81.4,,35B/35D,,,{},{},35B/35D,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171045,"{'06A-III': 99.4, '06B-I': 97.8, '06B-II': 90.8, '06A': 90.7, '06A-V': 89.9}",1,99.4,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(100.0)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001143345,"{'19F-I': 96.0, '19F': 95.7, '19F-III': 94.1, '19F-II': 92.9, '19F-IV': 88.9}",1,96.0,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001581355,"{'01': 6.6, '45': 6.4, '25F': 5.7, '25A': 5.5, '22F': 5.0}",3,6.6,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_012911425,"{'35B': 92.6, '33F': 33.7, '35C': 33.5, '34': 33.3, '35A': 33.1}",1,92.6,,35B/35D,,,{},{},35B/35D,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001154165,"{'06E': 98.0, '06B-III': 96.9, '06B-I': 46.0, '06A-III': 45.5, '06A-II': 44.5}",1,98.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900046805,"{'16F': 96.8, '07A': 96.4, '07F': 96.2, '18B': 43.0, '18C': 42.9}",1,96.8,,"Mixed serotypes- {'7F/7A', '16F'}",,,{},{},"Mixed serotypes- {'7F/7A', '16F'}",AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907170275,"{'14': 91.8, '36': 27.2, '19F-II': 24.4, '15B': 23.7, '15C': 23.6}",1,91.8,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001127605,"{'19F-I': 95.6, '19F': 95.3, '19F-III': 93.8, '19F-II': 92.5, '19F-IV': 88.5}",1,95.6,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171655,"{'19F-I': 99.6, '19F': 96.6, '19F-III': 96.6, '19F-II': 93.8, '19F-IV': 89.2}",1,99.6,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001585305,"{'12F': 97.0, '44': 93.7, '12B': 93.0, '12A': 80.7, '46': 77.6}",1,97.0,12F_12A_12B_44_46,12F_12A_12B_44_46,,[[5]],"{'wciI': [2, np.float64(100.0)]}",{'wciI': 2},12F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007787215,"{'01': 7.3, '45': 6.5, '25F': 5.8, '25A': 5.6, '22F': 5.4}",4,7.3,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001129725,"{'19F-I': 74.1, '19F': 73.5, '19F-III': 73.1, '19F-II': 70.7, '19F-IV': 67.1}",1,74.1,,19F,,,{},{},19F,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001338955,"{'19F-I': 96.0, '19F': 95.7, '19F-III': 94.1, '19F-II': 92.9, '19F-IV': 88.9}",1,96.0,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001335315,"{'32A': 97.5, '32F': 97.4, '06A-II': 40.4, '06A-VI': 40.3, '06B-II': 39.6}",1,97.5,,32F/32A,,,{},{},32F/32A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001109545,"{'06E': 99.7, '06B-III': 98.6, '06B-I': 46.4, '06A-III': 45.9, '06B-II': 45.2}",1,99.7,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001697005,"{'14': 87.5, '36': 28.9, '09L': 25.8, '09N': 24.5, '15B': 23.8}",1,87.5,,14,,,{},{},14,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171115,"{'06B-I': 99.5, '06A-III': 97.4, '06B-II': 90.1, '06A': 89.8, '06A-V': 88.2}",1,99.5,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(100.0)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001343615,"{'36': 10.5, '06A-IV': 6.5, '23B1': 5.7, '06B-I': 5.3, '06C': 5.2}",1,10.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001345395,"{'35F': 91.1, '47F': 67.7, '35B': 26.1, '29': 25.7, '34': 25.3}",1,91.1,,35F,,,{},{},35F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_019445785,"{'15A': 90.4, '15F': 68.8, '15C': 58.5, '15B': 58.4, '06C': 35.2}",1,90.4,15F_15A,15F_15A,,"[[11], [13], [15], [17]]","{'glf': 0, 'rmlB': 0, 'rmlD': 0, 'wcjE': 0}","{'glf': 'not_detected', 'rmlB': 'not_detected', 'rmlD': 'not_detected', 'wcjE': 'not_detected'}",15A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007785495,"{'33F': 75.2, '37': 74.3, '33A': 74.0, '33F2': 68.9, '35B': 32.1}",1,75.2,,"Mixed serotypes- {'37', '33F/33A'}",,,{},{},"Mixed serotypes- {'37', '33F/33A'}",AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007787435,"{'45': 6.4, '25F': 5.8, '25A': 5.6, '01': 5.3, '22F': 5.1}",3,6.4,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001719905,"{'19A-I': 99.4, '19A-II': 97.7, '19A': 88.0, '19A-III': 87.8, '19AF': 62.0}",1,99.4,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(95.25)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001346295,"{'14': 95.1, '15B': 24.3, '09L': 24.2, '15C': 24.2, '36': 23.8}",1,95.1,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001134245,"{'19F-II': 89.5, '19F': 88.8, '19F-I': 88.4, '19F-III': 87.2, '19F-IV': 85.2}",1,89.5,,19F,,,{},{},19F,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001117085,"{'19F-I': 95.3, '19F': 95.0, '19F-III': 93.5, '19F-II': 92.2, '19F-IV': 88.2}",1,95.3,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001167485,"{'36': 11.6, '06A-IV': 7.8, '20': 7.3, '06B-I': 6.6, '06C': 6.5}",2,11.6,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001719895,"{'06B-III': 76.7, '06E': 74.6, '06B-I': 41.2, '06A-III': 40.4, '06A-IV': 40.2}",1,76.7,6A_6B_6C_6D,6A_6B_6C_6D,,[[]],{}," wciN not found in isolate, possible variant","6A_6B_6C_6D:  wciN not found in isolate, possible variant",AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170945,"{'18C': 99.9, '18B': 99.8, '18F': 75.8, '18A': 62.4, '16F': 39.2}",1,99.9,,18C/18B,,,{},{},18C/18B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001167745,"{'10F': 98.2, '10C': 80.9, '10B': 22.4, '10A': 19.2, '20': 14.1}",1,98.2,,10F,,,{},{},10F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171565,"{'16F': 95.6, '28F': 42.3, '19F-II': 42.2, '19F-IV': 42.2, '19F': 41.2}",1,95.6,,16F,,,{},{},16F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001581645,"{'12F': 95.9, '12B': 93.3, '44': 92.9, '12A': 83.5, '46': 80.4}",1,95.9,12F_12A_12B_44_46,12F_12A_12B_44_46,,[[5]],"{'wciI': [2, np.float64(94.56)]}",{'wciI': 2},12F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001330175,"{'19F-I': 96.0, '19F': 95.7, '19F-III': 94.1, '19F-II': 92.9, '19F-IV': 88.9}",1,96.0,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001581485,"{'01': 27.3, '06C': 21.0, '06C-I': 21.0, '06A-II': 20.1, '06A-V': 20.1}",1,27.3,,"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",,,{},{},"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_002265095,"{'22F': 96.6, '22A': 73.4, '06A': 42.6, '06B': 42.1, '06A-I': 41.8}",1,96.6,,22F,,,{},{},22F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001211285,"{'01': 7.0, '45': 5.9, '25F': 5.7, '20': 5.5, '25A': 5.5}",2,7.0,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_002866375,"{'36': 10.8, '23B1': 6.6, '06A-IV': 6.2, '45': 6.0, '20': 5.9}",1,10.8,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907170125,"{'14': 92.2, '36': 27.7, '09L': 24.3, '15B': 24.2, '15C': 24.1}",1,92.2,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007786905,"{'45': 6.4, '01': 5.7, '25F': 5.3, '25A': 5.2, '22F': 5.1}",3,6.4,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907168245,"{'09A': 99.3, '09V': 99.1, '09N': 36.2, '09L': 34.4, '11F': 26.6}",1,99.3,,9A/9V,,,{},{},9A/9V,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171405,"{'21': 100.0, '22F': 35.7, '06A-IV': 32.5, '06A-II': 31.8, '06A-VI': 31.7}",1,100.0,,21,,,{},{},21,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_009721265,"{'19F-I': 99.9, '19F': 96.9, '19F-III': 96.9, '19F-II': 94.9, '19F-IV': 90.3}",1,99.9,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001115045,"{'36': 13.2, '20': 8.1, '06A-IV': 7.6, '01': 7.2, '06C': 6.2}",2,13.2,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001165885,"{'19F-I': 95.8, '19F': 95.5, '19F-III': 93.9, '19F-II': 92.7, '19F-IV': 88.7}",1,95.8,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001159885,"{'19F-I': 95.4, '19F': 95.2, '19F-III': 93.7, '19F-II': 92.3, '19F-IV': 88.3}",1,95.4,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001161945,"{'36': 9.4, '06A-IV': 6.7, '20': 6.6, '06C': 5.3, '06C-I': 5.2}",1,9.4,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001330395,"{'19F': 93.3, '19F-I': 93.3, '19F-III': 91.5, '19F-II': 90.2, '19F-IV': 86.2}",1,93.3,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001333975,"{'36': 9.1, '06A-IV': 6.8, '06C': 5.3, '06C-I': 5.3, '06A-II': 5.1}",1,9.1,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001347715,"{'06E': 100.0, '06B-III': 99.5, '06B-I': 46.9, '06A-III': 46.4, '06A-II': 45.4}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000355945,"{'01': 91.7, '19F': 32.3, '19F-I': 31.8, '19F-III': 31.6, '19F-II': 31.3}",1,91.7,,1,,,{},{},1,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901240465,"{'14': 91.2, '19F-IV': 25.9, '36': 24.9, '09L': 24.8, '09N': 24.7}",1,91.2,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000506605,"{'45': 6.3, '25F': 5.7, '25A': 5.5, '01': 5.4, '22F': 5.0}",2,6.3,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171215,"{'06B-I': 99.7, '06A-III': 97.6, '06B-II': 90.3, '06A': 89.8, '06A-V': 88.4}",1,99.7,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(100.0)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170585,"{'06B-I': 99.7, '06A-III': 97.6, '06B-II': 90.3, '06A': 89.8, '06A-V': 88.4}",1,99.7,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(100.0)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001330095,"{'19F-I': 84.2, '19F': 83.6, '19F-III': 82.9, '19F-II': 80.8, '19F-IV': 76.7}",1,84.2,,19F,,,{},{},19F,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001171605,"{'19F-I': 96.0, '19F': 95.7, '19F-III': 94.1, '19F-II': 92.9, '19F-IV': 88.9}",1,96.0,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171005,"{'19F-II': 99.8, '19F': 95.3, '19F-III': 94.3, '19F-I': 94.0, '19F-IV': 93.3}",1,99.8,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001581245,"{'25F': 21.8, '25A': 21.4, '38': 12.6, '36': 8.8, '22F': 7.2}",1,21.8,,"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",,,{},{},"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901236495,"{'06E': 98.5, '06B-III': 97.6, '06B-I': 46.6, '06A-III': 46.0, '06A-II': 45.0}",1,98.5,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170335,"{'15A': 98.6, '15F': 73.8, '15C': 62.1, '15B': 62.0, '23F': 31.9}",1,98.6,15F_15A,15F_15A,,"[[11], [13], [15], [17]]","{'glf': 0, 'rmlB': 0, 'rmlD': 0, 'wcjE': 0}","{'glf': 'not_detected', 'rmlB': 'not_detected', 'rmlD': 'not_detected', 'wcjE': 'not_detected'}",15A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901245785,"{'19A-I': 99.4, '19A-II': 97.7, '19A': 88.0, '19A-III': 87.8, '19AF': 62.0}",1,99.4,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(95.25)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907167295,"{'14': 91.3, '36': 26.4, '09L': 25.6, '09N': 24.8, '15B': 23.4}",1,91.3,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001345975,"{'06E': 100.0, '06B-III': 98.1, '06B-I': 45.7, '06A-III': 45.2, '06A-II': 44.2}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001129045,"{'19F-I': 95.8, '19F': 95.5, '19F-III': 93.9, '19F-II': 92.7, '19F-IV': 88.7}",1,95.8,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_003933515,"{'35A': 87.8, '35C': 83.9, '42': 83.3, '33A': 43.0, '33F': 42.3}",1,87.8,,35A/35C/42,,,{},{},35A/35C/42,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001130525,"{'10A': 99.4, '10B': 67.1, '10C': 27.7, '10F': 18.1, '06B-I': 13.5}",1,99.4,,10A,,,{},{},10A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170095,"{'10A': 100.0, '10B': 66.8, '10C': 27.5, '10F': 17.9, '22F': 14.6}",1,100.0,,10A,,,{},{},10A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001336715,"{'17F': 93.3, '06A-III': 45.3, '06A-IV': 45.2, '06B-I': 45.1, '06A': 44.5}",1,93.3,,17F,,,{},{},17F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001074475,"{'19A': 99.3, '19A-III': 99.1, '19A-I': 86.2, '19A-II': 83.9, '19AF': 57.2}",1,99.3,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(100.0)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171595,"{'19F-I': 99.9, '19F': 96.9, '19F-III': 96.9, '19F-II': 94.1, '19F-IV': 89.5}",1,99.9,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901237205,"{'14': 95.9, '36': 26.0, '09L': 25.5, '09N': 24.5, '15B': 24.3}",1,95.9,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171295,"{'19F-I': 99.6, '19F': 96.6, '19F-III': 96.6, '19F-II': 93.8, '19F-IV': 89.2}",1,99.6,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171205,"{'35F': 99.3, '47F': 74.6, '34': 26.7, '35B': 26.6, '29': 22.5}",1,99.3,,35F,,,{},{},35F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_020037995,"{'10A': 38.4, '06A-IV': 24.7, '10B': 24.1, '06B-I': 23.9, '06A-III': 23.6}",1,38.4,,"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",,,{},{},"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_003933595,"{'23B': 74.1, '23B1': 48.6, '23F': 38.3, '06A-IV': 33.9, '23A': 33.0}",1,74.1,,23B,,,{},{},23B,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_008039015,"{'01': 6.2, '25F': 5.8, '45': 5.8, '25A': 5.6, '22F': 5.2}",2,6.2,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_003933665,"{'15B': 61.9, '15C': 61.8, '15A': 36.2, '23A': 29.8, '14': 29.1}",1,61.9,,"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",,,{},{},"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001299795,"{'19F-I': 95.7, '19F': 95.4, '19F-III': 93.8, '19F-II': 92.6, '19F-IV': 88.6}",1,95.7,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901242155,"{'06A-II': 83.4, '06A-VI': 83.4, '06A-III': 83.3, '06A-V': 82.6, '06B-I': 81.9}",1,83.4,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(93.22)]}",{'wciN': 'a'},6A/6B,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001719865,"{'19F-I': 98.0, '19F': 97.3, '19F-III': 96.8, '19F-II': 95.3, '19F-IV': 90.4}",1,98.0,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001173885,"{'25A': 3.5, '25F': 3.5, '01': 3.1, '45': 3.0, '22F': 2.9}",1,3.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001138045,"{'35F': 99.3, '47F': 74.6, '34': 26.7, '35B': 26.2, '29': 22.5}",1,99.3,,35F,,,{},{},35F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901254065,"{'18C': 99.1, '18B': 99.0, '18F': 75.9, '18A': 62.9, '16F': 39.1}",1,99.1,,18C/18B,,,{},{},18C/18B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901248715,"{'11D': 76.8, '11A': 75.5, '11F': 42.4, '11B': 33.4, '11C': 30.1}",1,76.8,,11A/11D,,,{},{},11A/11D,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170145,"{'14': 92.7, '36': 29.9, '09L': 25.6, '09N': 24.7, '15B': 24.3}",1,92.7,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001083665,"{'25F': 6.5, '25A': 6.3, '45': 6.2, '22F': 4.9, '38': 4.9}",2,6.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001091745,"{'36': 10.6, '20': 7.5, '06A-IV': 6.7, '45': 6.3, '06B-I': 5.6}",1,10.6,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900172395,"{'19F-I': 99.6, '19F': 96.6, '19F-III': 96.6, '19F-II': 93.8, '19F-IV': 89.4}",1,99.6,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001336035,"{'19F': 95.5, '19F-I': 95.5, '19F-III': 93.9, '19F-II': 92.4, '19F-IV': 88.5}",1,95.5,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001112165,"{'19F-I': 93.2, '19F': 92.9, '19F-III': 91.5, '19F-II': 90.7, '19F-IV': 88.8}",1,93.2,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171145,"{'06E': 100.0, '06B-III': 99.4, '06B-I': 46.8, '06A-III': 46.3, '06A-II': 45.3}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907166905,"{'09A': 97.6, '09V': 97.4, '09N': 34.8, '09L': 33.7, '11F': 26.6}",1,97.6,,9A/9V,,,{},{},9A/9V,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001165905,"{'06A-III': 91.0, '06A': 90.8, '06B-I': 89.8, '06B-II': 89.5, '06A-II': 89.2}",2,91.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(100.0)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001174085,"{'06E': 99.8, '06B-III': 99.4, '06B-I': 47.0, '06A-III': 46.5, '06A-II': 45.5}",1,99.8,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001150725,"{'19F-I': 95.7, '19F': 95.4, '19F-III': 93.9, '19F-II': 92.6, '19F-IV': 88.6}",1,95.7,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007787035,"{'01': 5.7, '20': 5.4, '45': 5.4, '22F': 5.0, '25F': 5.0}",2,5.7,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001581425,"{'06A-II': 85.4, '06A-VI': 85.3, '06A-III': 85.0, '06B-I': 84.0, '06A-V': 83.2}",1,85.4,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(93.22)]}",{'wciN': 'a'},6A/6B,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001112045,"{'06E': 99.9, '06B-III': 95.1, '06A-I': 42.6, '06B-I': 42.6, '06B': 42.2}",1,99.9,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007784675,"{'36': 10.8, '23B1': 6.8, '06A-IV': 6.7, '45': 6.6, '20': 6.0}",1,10.8,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001100545,"{'06E': 100.0, '06B-III': 95.0, '06A-I': 42.6, '06B-I': 42.4, '06B': 42.2}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001338875,"{'45': 5.1, '25F': 4.8, '25A': 4.6, '35B': 3.3, '38': 3.3}",3,5.1,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001087365,"{'38': 86.9, '25F': 83.4, '25A': 82.6, '36': 11.9, '20': 7.9}",1,86.9,25F_25A_38,25F_25A_38,,"[[0], [18]]","{'wcyD': ['b: 22.59'], 'wcyV': np.float64(4.69)}","{'wcyD': 0, 'wcyV': 'not_detected'}",25F_25A_38,RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007785265,"{'01': 6.3, '45': 5.9, '25F': 5.7, '20': 5.5, '25A': 5.5}",3,6.3,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001336835,"{'13': 95.3, '36': 31.5, '09L': 26.6, '14': 25.7, '09N': 25.6}",1,95.3,,13,,,{},{},13,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001108585,"{'06E': 99.9, '06B-III': 98.3, '06B-I': 45.9, '06A-III': 45.4, '06A-II': 44.4}",1,99.9,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_002889155,"{'19F-I': 95.5, '19F': 95.2, '19F-III': 93.7, '19F-II': 92.4, '19F-IV': 88.4}",1,95.5,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001341295,"{'35B': 94.6, '33F': 33.9, '35C': 33.6, '35A': 33.2, '34': 33.1}",1,94.6,,35B/35D,,,{},{},35B/35D,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901243345,"{'12F': 96.0, '12B': 93.4, '44': 93.0, '12A': 84.5, '46': 81.4}",1,96.0,12F_12A_12B_44_46,12F_12A_12B_44_46,,[[5]],"{'wciI': [2, np.float64(94.56)]}",{'wciI': 2},12F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001581515,"{'01': 6.3, '45': 6.3, '25F': 5.7, '25A': 5.5, '22F': 5.0}",3,6.3,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007784825,"{'01': 6.8, '45': 6.5, '25F': 5.8, '25A': 5.6, '22F': 5.5}",3,6.8,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_012911295,"{'35B': 67.3, '34': 33.0, '33F': 32.8, '35C': 32.7, '35A': 32.3}",1,67.3,,"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",,,{},{},"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170525,"{'06B-I': 99.6, '06A-III': 97.5, '06B-II': 90.2, '06A': 89.8, '06A-V': 88.3}",1,99.6,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(100.0)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001128765,"{'19A': 99.8, '19A-III': 99.6, '19A-I': 86.0, '19A-II': 83.5, '19AF': 57.2}",1,99.8,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(100.0)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001715895,"{'12F': 94.6, '12B': 92.2, '44': 91.7, '12A': 79.8, '46': 76.7}",1,94.6,12F_12A_12B_44_46,12F_12A_12B_44_46,,[[5]],"{'wciI': [2, np.float64(94.56)]}",{'wciI': 2},12F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001123585,"{'06E': 100.0, '06B-III': 94.9, '06A-I': 42.6, '06B': 42.2, '06B-I': 42.2}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_003934015,"{'35A': 86.3, '35C': 82.7, '42': 82.0, '33A': 44.6, '33F': 44.1}",1,86.3,,35A/35C/42,,,{},{},35A/35C/42,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001330495,"{'19F-I': 95.4, '19F': 95.2, '19F-III': 93.7, '19F-II': 92.3, '19F-IV': 88.3}",1,95.4,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901221615,"{'01': 92.0, '19F': 33.3, '19F-I': 32.6, '19F-III': 32.5, '19F-II': 32.4}",1,92.0,,1,,,{},{},1,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007787575,"{'19A-II': 97.6, '19A-I': 95.3, '19A': 83.6, '19A-III': 83.4, '19AF': 60.9}",1,97.6,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(95.25)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_008039165,"{'45': 6.5, '25F': 5.8, '25A': 5.6, '22F': 5.2, '38': 4.9}",3,6.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_019446195,"{'22F': 98.5, '22A': 73.4, '06A': 42.6, '06B': 42.1, '06A-II': 41.9}",1,98.5,,22F,,,{},{},22F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001092685,"{'19F': 95.5, '19F-I': 95.5, '19F-III': 93.9, '19F-II': 92.4, '19F-IV': 88.5}",1,95.5,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001106205,"{'25F': 5.7, '45': 5.6, '20': 5.5, '25A': 5.5, '22F': 5.1}",2,5.7,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001096165,"{'18C': 88.6, '18B': 88.5, '18F': 78.1, '18A': 60.1, '16F': 37.9}",1,88.6,,18C/18B,,,{},{},18C/18B,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001145425,"{'33B': 89.8, '33D': 89.7, '35B': 33.1, '33F2': 30.0, '22F': 26.5}",1,89.8,,"Mixed serotypes- {'33B', '33D'}",,,{},{},"Mixed serotypes- {'33B', '33D'}",AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000173595,"{'14': 99.9, '36': 26.0, '15B': 24.3, '15C': 24.2, '09L': 23.7}",1,99.9,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001329915,"{'06E': 96.4, '06B-III': 94.6, '06B-I': 45.0, '06A-III': 44.4, '06A-II': 43.8}",1,96.4,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000385775,"{'23F': 95.9, '23A': 63.0, '23B': 48.2, '06A-IV': 48.2, '28A': 46.7}",1,95.9,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001165485,"{'23A': 94.2, '23F': 66.0, '23B': 45.8, '19F-II': 39.1, '15B': 38.3}",1,94.2,,23A,,,{},{},23A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001330155,"{'19F-I': 95.6, '19F': 95.3, '19F-III': 93.8, '19F-II': 92.5, '19F-IV': 88.5}",1,95.6,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907172315,"{'14': 82.5, '36': 25.3, '09L': 25.0, '09N': 24.0, '15B': 23.5}",1,82.5,,14,,,{},{},14,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907169705,"{'14': 92.6, '36': 28.7, '09L': 24.5, '15B': 24.2, '15C': 24.1}",1,92.6,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_002866105,"{'01': 6.9, '45': 5.9, '25F': 5.7, '20': 5.5, '25A': 5.5}",2,6.9,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900060235,"{'15C': 95.1, '15B': 95.0, '15A': 63.3, '15F': 55.3, '23B': 52.4}",1,95.1,,15B/15C,,,{},{},15B/15C,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000983075,"{'14': 94.6, '36': 26.2, '09L': 25.4, '09N': 24.6, '15B': 24.2}",1,94.6,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001084445,"{'28F': 98.6, '28A': 92.2, '23F': 47.6, '16F': 45.9, '06B-I': 42.5}",1,98.6,,28F/28A,,,{},{},28F/28A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001110145,"{'14': 91.4, '36': 25.8, '19F-II': 25.3, '19F-I': 23.9, '19F': 23.4}",1,91.4,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170165,"{'23F': 98.4, '23A': 65.3, '28A': 48.0, '06A': 45.5, '28F': 45.4}",1,98.4,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007786525,"{'03': 97.4, '01': 16.9, '20': 15.5, '09N': 15.3, '09L': 15.1}",1,97.4,,3,,,{},{},3,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007785355,"{'45': 6.4, '01': 5.9, '25F': 5.8, '25A': 5.6, '22F': 5.3}",2,6.4,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_003968975,"{'15C': 47.9, '15B': 47.8, '15A': 28.9, '14': 25.2, '23A': 25.1}",1,47.9,,"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",,,{},{},"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001925185,"{'06E': 100.0, '06B-III': 98.8, '06B-I': 46.4, '06A-III': 45.9, '06A-II': 44.9}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_002866205,"{'45': 5.9, '20': 5.8, '25F': 5.8, '25A': 5.6, '38': 4.9}",2,5.9,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_018253935,"{'24F2': 99.7, '24B': 88.5, '24F': 87.0, '24A': 71.0, '07B': 56.8}",1,99.7,,24F/24B,,,{},{},24F/24B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000762465,"{'45': 6.1, '25F': 5.7, '25A': 5.5, '01': 5.1, '22F': 4.9}",2,6.1,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007787075,"{'01': 6.2, '45': 5.9, '25F': 5.7, '20': 5.5, '25A': 5.5}",3,6.2,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001121565,"{'36': 7.8, '20': 5.8, '06A-IV': 5.6, '45': 4.8, '38': 4.5}",1,7.8,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001335875,"{'23F': 94.6, '23A': 63.7, '28A': 47.7, '23B': 47.0, '06A': 46.4}",1,94.6,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001341115,"{'19A-I': 99.4, '19A-II': 97.7, '19A': 88.0, '19A-III': 87.8, '19AF': 62.0}",1,99.4,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(95.25)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907171705,"{'06E': 95.2, '14': 92.1, '06B-III': 91.7, '06B-II': 45.6, '06A-I': 45.3}",1,95.2,,"Mixed serotypes- {'14', '6A_6B_6C_6D'}",,,{},{},"Mixed serotypes- {'14', '6A_6B_6C_6D'}",AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001165985,"{'06E': 100.0, '06B-III': 93.6, '06A-I': 42.6, '06B': 42.2, '06B-I': 41.2}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001125165,"{'14': 89.8, '36': 29.3, '09L': 23.9, '09N': 23.1, '19F-II': 22.2}",1,89.8,,14,,,{},{},14,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_012911035,"{'35B': 79.6, '33F': 33.3, '35C': 33.2, '34': 33.0, '35A': 32.8}",1,79.6,,35B/35D,,,{},{},35B/35D,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001167025,"{'23F': 94.0, '23A': 63.5, '28A': 48.5, '23B': 47.0, '06A': 46.2}",1,94.0,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001909205,"{'03': 95.2, '36': 16.9, '20': 15.2, '01': 15.0, '09L': 14.1}",1,95.2,,3,,,{},{},3,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901244255,"{'19A-I': 99.4, '19A-II': 97.7, '19A': 88.0, '19A-III': 87.8, '19AF': 62.0}",1,99.4,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(95.25)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001340655,"{'18C': 86.4, '18B': 86.3, '18F': 74.9, '18A': 57.6, '16F': 36.0}",1,86.4,,18C/18B,,,{},{},18C/18B,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007785405,"{'45': 6.5, '25F': 5.8, '25A': 5.6, '01': 5.4, '38': 4.9}",2,6.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001100265,"{'19F-I': 95.8, '19F': 95.5, '19F-III': 93.9, '19F-II': 92.7, '19F-IV': 88.7}",1,95.8,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171365,"{'06A-I': 99.0, '19F-I': 97.4, '19F': 95.1, '19F-III': 95.1, '06B': 94.4}",1,99.0,,"Mixed serotypes- {'19F', '6A_6B_6C_6D'}",,,{},{},"Mixed serotypes- {'19F', '6A_6B_6C_6D'}",AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000230355,"{'14': 99.7, '09L': 27.4, '36': 26.0, '09N': 24.7, '15B': 24.3}",1,99.7,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170185,"{'11D': 100.0, '11A': 97.2, '11F': 42.0, '11C': 35.9, '11B': 34.4}",1,100.0,,11A/11D,,,{},{},11A/11D,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001113445,"{'25F': 4.6, '12A': 4.5, '25A': 4.5, '46': 4.5, '45': 4.1}",1,4.6,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001083265,"{'15C': 95.8, '15B': 95.7, '15A': 61.2, '15F': 47.6, '23A': 34.7}",1,95.8,,15B/15C,,,{},{},15B/15C,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001132885,"{'23F': 85.7, '23A': 56.9, '28A': 45.8, '23B': 43.7, '06A': 43.3}",1,85.7,,23F,,,{},{},23F,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001083385,"{'14': 95.1, '36': 26.3, '09L': 24.4, '15B': 24.3, '15C': 24.2}",1,95.1,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001207515,"{'06E': 100.0, '06B-III': 99.6, '06B-I': 47.0, '06A-III': 46.5, '06A-II': 45.5}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001156865,"{'05': 95.2, '45': 21.2, '12A': 19.7, '46': 19.6, '04': 19.3}",1,95.2,,5,,,{},{},5,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900052155,"{'19A': 99.3, '19A-III': 99.1, '19A-I': 86.2, '19A-II': 84.0, '19AF': 57.2}",1,99.3,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(100.0)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170365,"{'09A': 99.7, '09V': 99.5, '09N': 37.8, '09L': 36.8, '11F': 26.6}",1,99.7,,9A/9V,,,{},{},9A/9V,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_019446205,"{'33F': 99.8, '33A': 97.3, '33F2': 70.7, '35C': 42.6, '42': 41.6}",1,99.8,,33F/33A,,,{},{},33F/33A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900067725,"{'14': 81.1, '36': 21.8, '09L': 19.7, '09N': 18.8, '13': 18.7}",1,81.1,,14,,,{},{},14,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001099865,"{'19F-I': 95.8, '19F': 95.5, '19F-III': 93.9, '19F-II': 92.7, '19F-IV': 88.8}",1,95.8,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907167015,"{'09A': 99.4, '09V': 99.2, '09N': 36.3, '09L': 34.6, '11F': 26.5}",1,99.4,,9A/9V,,,{},{},9A/9V,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001169185,"{'19F-I': 95.6, '19F': 95.3, '19F-III': 93.8, '19F-II': 92.5, '19F-IV': 88.5}",1,95.6,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170735,"{'06A-I': 100.0, '06B': 94.5, '06A-V': 89.3, '06A': 87.1, '06A-III': 86.0}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(96.61)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001909835,"{'03': 95.2, '36': 17.2, '01': 16.3, '20': 15.8, '09N': 15.2}",1,95.2,,3,,,{},{},3,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001135505,"{'06C-I': 87.3, '06C': 87.2, '06D': 84.6, '06A': 76.9, '06A-IV': 74.8}",1,87.3,6A_6B_6C_6D,6A_6B_6C_6D,,[[0]],{'wciN': ['b: 83.5']},{'wciN': 0},6A_6B_6C_6D,RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901220395,"{'23F': 93.6, '23A': 63.1, '28A': 48.1, '23B': 46.6, '06A-III': 46.4}",1,93.6,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001130505,"{'06A-III': 98.3, '06B-I': 96.7, '06A': 90.6, '06B-II': 90.2, '06A-V': 89.3}",1,98.3,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(100.0)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007785245,"{'01': 6.8, '45': 6.4, '25F': 5.6, '25A': 5.4, '22F': 5.1}",4,6.8,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001087605,"{'32F': 97.5, '32A': 97.4, '06A': 37.8, '27': 37.3, '06D': 37.2}",1,97.5,,32F/32A,,,{},{},32F/32A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170535,"{'34': 98.9, '06A-II': 96.4, '06A-VI': 96.4, '06B-II': 89.4, '06A-V': 88.7}",1,98.9,,"Mixed serotypes- {'6A_6B_6C_6D', '34'}",,,{},{},"Mixed serotypes- {'6A_6B_6C_6D', '34'}",AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907167055,"{'09A': 99.4, '09V': 99.2, '09N': 37.0, '09L': 35.4, '11F': 26.6}",1,99.4,,9A/9V,,,{},{},9A/9V,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001330715,"{'06E': 100.0, '06B-III': 97.5, '06B-I': 44.8, '06A-III': 44.3, '06B-II': 43.5}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001581475,"{'35B': 99.9, '33F': 33.6, '35C': 33.4, '34': 33.1, '35A': 33.0}",1,99.9,,35B/35D,,,{},{},35B/35D,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001161325,"{'36': 6.3, '06A-IV': 4.7, '12A': 4.5, '46': 4.5, '20': 3.7}",1,6.3,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001336335,"{'36': 11.5, '20': 8.4, '06A-IV': 7.5, '45': 6.4, '06C': 6.3}",1,11.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001584975,"{'12F': 97.0, '44': 93.7, '12B': 93.0, '12A': 80.7, '46': 77.6}",1,97.0,12F_12A_12B_44_46,12F_12A_12B_44_46,,[[5]],"{'wciI': [2, np.float64(100.0)]}",{'wciI': 2},12F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001141885,"{'06A-I': 98.5, '06B': 94.4, '06A-V': 89.0, '06A': 87.4, '06A-III': 85.5}",1,98.5,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(96.61)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000334855,"{'01': 98.9, '19F': 32.0, '19F-I': 31.5, '19F-III': 31.3, '19F-II': 31.0}",1,98.9,,1,,,{},{},1,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001719805,"{'06A-II': 82.5, '06A-VI': 82.4, '06A-III': 82.3, '06A-V': 81.2, '06B-I': 81.0}",1,82.5,6A_6B_6C_6D,6A_6B_6C_6D,,[[0]],{'wciN': ['a: 88.74']},{'wciN': 0},6A_6B_6C_6D,RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901246385,"{'08': 98.4, '06A-II': 24.5, '02': 24.4, '06A-VI': 24.4, '06B-II': 23.9}",1,98.4,,8,,,{},{},8,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001342895,"{'19A-I': 99.3, '19A-II': 97.7, '19A': 87.9, '19A-III': 87.7, '19AF': 62.0}",1,99.3,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(95.25)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001164845,"{'06A-II': 87.1, '06A-VI': 87.1, '06A': 85.9, '06A-IV': 85.0, '06A-V': 84.8}",1,87.1,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(96.5)]}",{'wciN': 'a'},6A/6B,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_020038085,"{'23A': 98.7, '23F': 69.0, '24A': 48.2, '24B': 47.9, '19F-I': 47.8}",1,98.7,,23A,,,{},{},23A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001097925,"{'04': 98.3, '45': 32.3, '12F': 23.8, '44': 23.6, '12A': 22.7}",1,98.3,,4,,,{},{},4,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001301615,"{'35B': 99.8, '33F': 33.6, '35C': 33.3, '34': 33.1, '35A': 32.9}",1,99.8,,35B/35D,,,{},{},35B/35D,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001336235,"{'23F': 69.8, '23A': 46.2, '06B-I': 38.4, '06A-III': 37.9, '06B-II': 37.3}",1,69.8,,"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",,,{},{},"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000167615,"{'04': 99.8, '45': 28.1, '12A': 26.9, '46': 26.8, '12F': 23.5}",1,99.8,,4,,,{},{},4,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001329595,"{'23F': 96.5, '23A': 63.2, '28A': 47.2, '23B': 46.4, '06A-IV': 46.4}",1,96.5,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171065,"{'23F': 99.4, '23A': 65.2, '23B': 47.9, '28A': 47.8, '06A-V': 45.8}",1,99.4,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000355965,"{'01': 94.2, '19F': 32.3, '19F-I': 31.8, '19F-III': 31.6, '19F-II': 31.3}",1,94.2,,1,,,{},{},1,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_019446125,"{'35B': 99.2, '33F': 33.7, '35C': 33.5, '34': 33.3, '35A': 33.1}",1,99.2,,35B/35D,,,{},{},35B/35D,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170075,"{'23F': 94.0, '23A': 62.8, '23B': 49.5, '06A-IV': 49.3, '06B-II': 49.1}",1,94.0,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170405,"{'19A-II': 85.5, '19A-I': 82.6, '19A': 70.9, '19A-III': 70.8, '19AF': 56.4}",1,85.5,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(95.25)]}",{'wzy': 1},19A,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901251615,"{'15C': 86.4, '15B': 86.3, '15A': 63.7, '15F': 48.9, '23A': 30.2}",1,86.4,,15B/15C,,,{},{},15B/15C,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001329735,"{'06E': 99.9, '06B-III': 97.2, '06B-I': 44.6, '06A-III': 44.1, '06B-II': 43.3}",1,99.9,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_002889095,"{'09A': 99.7, '09V': 99.5, '09N': 36.3, '09L': 35.3, '11F': 26.6}",1,99.7,,9A/9V,,,{},{},9A/9V,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_002922975,"{'15A': 99.8, '15F': 74.1, '15C': 61.9, '15B': 61.8, '23F': 31.7}",1,99.8,15F_15A,15F_15A,,"[[11], [13], [15], [17]]","{'glf': 0, 'rmlB': 0, 'rmlD': 0, 'wcjE': 0}","{'glf': 'not_detected', 'rmlB': 'not_detected', 'rmlD': 'not_detected', 'wcjE': 'not_detected'}",15A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001165645,"{'23F': 94.5, '23A': 63.6, '06A-IV': 49.4, '23B': 48.4, '28A': 47.7}",1,94.5,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001135465,"{'22F': 4.9, '25F': 4.8, '01': 4.7, '25A': 4.6, '38': 3.7}",1,4.9,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001121705,"{'06E': 99.6, '06B-III': 99.0, '06B-I': 46.7, '06A-III': 46.2, '06A-II': 45.1}",1,99.6,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001167805,"{'15A': 97.5, '15F': 73.6, '15C': 61.6, '15B': 61.5, '23F': 31.3}",1,97.5,15F_15A,15F_15A,,"[[11], [13], [15], [17]]","{'glf': 0, 'rmlB': 0, 'rmlD': 0, 'wcjE': 0}","{'glf': 'not_detected', 'rmlB': 'not_detected', 'rmlD': 'not_detected', 'wcjE': 'not_detected'}",15A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171095,"{'19F-I': 99.7, '19F': 96.7, '19F-III': 96.7, '19F-II': 93.9, '19F-IV': 89.3}",1,99.7,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001168245,"{'23F': 85.7, '23A': 57.1, '06A-IV': 53.2, '06B-II': 51.6, '06A-V': 50.8}",1,85.7,,23F,,,{},{},23F,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001089845,"{'07C': 99.5, '07B': 73.1, '40': 70.9, '24B': 48.9, '24F': 48.7}",1,99.5,,7C,,,{},{},7C,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001141685,"{'10B': 99.5, '10A': 65.3, '10F': 20.1, '10C': 18.8, '47A': 12.6}",1,99.5,,10B,,,{},{},10B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_003934025,"{'23B': 70.8, '23B1': 44.7, '23F': 38.0, '06A-IV': 33.6, '28A': 32.6}",1,70.8,,23B,,,{},{},23B,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001095905,"{'19F-I': 95.8, '19F': 95.5, '19F-III': 94.0, '19F-II': 92.7, '19F-IV': 88.7}",1,95.8,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901267475,"{'23F': 92.6, '23A': 61.3, '28A': 48.1, '23B': 46.8, '06A-IV': 46.6}",1,92.6,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000762685,"{'09N': 97.8, '09L': 87.8, '09A': 32.7, '09V': 32.7, '36': 31.9}",1,97.8,,9N/9L,,,{},{},9N/9L,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901244915,"{'36': 12.0, '01': 7.8, '20': 7.3, '06A-IV': 7.2, '45': 6.7}",1,12.0,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901246185,"{'06A-II': 92.5, '06A-VI': 92.5, '06B-II': 87.1, '06A-V': 86.6, '06A-III': 85.6}",1,92.5,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(93.22)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001196105,"{'06E': 100.0, '06B-III': 99.1, '06B-I': 46.7, '06A-III': 46.2, '06A-II': 45.2}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907170285,"{'14': 91.8, '36': 28.5, '09L': 25.7, '09N': 25.4, '15B': 24.2}",1,91.8,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_012911485,"{'35B': 69.6, '33F': 33.3, '34': 33.3, '35C': 33.2, '35A': 32.8}",1,69.6,,"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",,,{},{},"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001168645,"{'06E': 91.4, '06B-III': 86.3, '06A-I': 39.8, '06B': 39.6, '06B-I': 38.6}",1,91.4,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901247115,"{'19A-I': 99.4, '19A-II': 97.7, '19A': 88.0, '19A-III': 87.8, '19AF': 62.0}",1,99.4,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(95.25)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001140065,"{'01': 6.0, '45': 5.7, '22F': 4.8, '36': 4.7, '12A': 4.5}",2,6.0,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000203715,"{'06C-I': 88.4, '06C': 88.3, '06D': 86.9, '06A-I': 77.7, '06B': 77.4}",1,88.4,6A_6B_6C_6D,6A_6B_6C_6D,,[[2]],"{'wciN': ['b', np.float64(91.3)]}",{'wciN': 'b'},6C/6D,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_003934055,"{'35A': 92.3, '35C': 88.0, '42': 87.4, '33A': 46.1, '33F': 45.6}",1,92.3,,35A/35C/42,,,{},{},35A/35C/42,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_012911365,"{'35B': 70.1, '34': 33.3, '33F': 33.0, '35C': 32.9, '35A': 32.5}",1,70.1,,35B/35D,,,{},{},35B/35D,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001149045,"{'19F-I': 87.7, '19F': 87.2, '19F-III': 85.9, '19F-II': 84.6, '19F-IV': 80.6}",1,87.7,,19F,,,{},{},19F,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170555,"{'14': 99.8, '09L': 27.1, '36': 26.1, '09N': 24.3, '15B': 24.3}",1,99.8,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007786645,"{'45': 6.5, '25F': 5.8, '25A': 5.6, '22F': 5.5, '01': 4.9}",3,6.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170575,"{'01': 6.2, '45': 5.7, '20': 5.5, '25F': 5.4, '25A': 5.2}",1,6.2,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001719885,"{'03': 97.4, '01': 17.3, '20': 15.5, '09N': 15.3, '09L': 15.1}",1,97.4,,3,,,{},{},3,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170825,"{'14': 99.7, '09L': 27.2, '36': 26.1, '15B': 24.3, '09N': 24.2}",1,99.7,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_002866445,"{'45': 6.5, '25F': 5.8, '25A': 5.6, '01': 5.5, '22F': 5.4}",2,6.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001345915,"{'23F': 96.8, '23A': 66.4, '28A': 47.4, '06A': 46.0, '28F': 45.1}",1,96.8,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907172115,"{'14': 92.7, '36': 28.4, '15B': 24.3, '15C': 24.2, '09L': 23.9}",1,92.7,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001157805,"{'35B': 99.0, '33F': 33.7, '35C': 33.5, '34': 33.3, '35A': 33.1}",1,99.0,,35B/35D,,,{},{},35B/35D,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907167505,"{'09A': 99.7, '09V': 99.5, '09N': 35.1, '09L': 33.9, '11F': 26.6}",1,99.7,,9A/9V,,,{},{},9A/9V,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001097505,"{'06E': 100.0, '06B-III': 95.0, '06A-I': 42.6, '06B-I': 42.3, '06B': 42.2}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001100665,"{'06E': 100.0, '06B-III': 95.9, '06B-I': 43.2, '06A-III': 42.7, '06A-I': 42.3}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001129085,"{'06A-IV': 2.2, '01': 1.3, '14': 0.1}",1,2.2,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171485,"{'19F-I': 99.7, '19F': 96.7, '19F-III': 96.7, '19F-II': 93.9, '19F-IV': 89.3}",1,99.7,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001925165,"{'06E': 100.0, '06B-III': 95.9, '06B-I': 43.4, '06A-III': 42.9, '06B': 42.2}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001114505,"{'25F': 5.6, '25A': 5.4, '22F': 4.9, '35B': 4.4, '38': 4.4}",1,5.6,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001100085,"{'19F-I': 73.0, '19F': 72.8, '19F-II': 71.8, '19F-III': 71.8, '19F-IV': 67.8}",1,73.0,,19F,,,{},{},19F,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001329555,"{'06E': 100.0, '06B-III': 99.6, '06B-I': 47.1, '06A-III': 46.6, '06A-II': 45.6}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907167925,"{'14': 93.4, '36': 27.0, '09L': 24.5, '15B': 24.3, '15C': 24.2}",1,93.4,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900035615,"{'19A-I': 99.1, '19A-II': 97.9, '19A': 91.5, '19A-III': 91.3, '19AF': 62.3}",1,99.1,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(95.25)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907171695,"{'14': 92.2, '36': 28.6, '09L': 24.7, '15B': 24.2, '15C': 24.1}",1,92.2,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001153705,"{'45': 94.7, '04': 38.8, '06A-II': 31.8, '06A-VI': 31.7, '06B-I': 31.6}",1,94.7,,45,,,{},{},45,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170635,"{'06A-II': 99.8, '06A-VI': 99.8, '06B-II': 91.8, '06A-V': 91.1, '06A-III': 89.6}",1,99.8,6A_6B_6C_6D,6A_6B_6C_6D,,[[0]],{'wciN': ['a: 89.84']},{'wciN': 0},6A_6B_6C_6D,RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171125,"{'14': 99.9, '09L': 26.5, '36': 26.0, '09N': 24.4, '15B': 24.2}",1,99.9,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001163405,"{'14': 89.8, '36': 28.9, '09L': 23.5, '09N': 22.5, '19F-II': 22.2}",1,89.8,,14,,,{},{},14,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001088405,"{'19F-I': 95.9, '19F': 95.6, '19F-III': 94.0, '19F-II': 92.8, '19F-IV': 88.8}",1,95.9,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_010604175,"{'35B': 97.7, '33F': 33.5, '34': 33.3, '35C': 33.3, '35A': 32.9}",1,97.7,,35B/35D,,,{},{},35B/35D,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001167685,"{'35B': 99.6, '33F': 33.6, '35C': 33.3, '34': 33.1, '35A': 32.9}",1,99.6,,35B/35D,,,{},{},35B/35D,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001129605,"{'19F-I': 95.8, '19F': 95.5, '19F-III': 93.9, '19F-II': 92.7, '19F-IV': 88.7}",1,95.8,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900171235,"{'11D': 100.0, '11A': 97.2, '11F': 42.0, '11C': 35.9, '11B': 34.4}",1,100.0,,11A/11D,,,{},{},11A/11D,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001161345,"{'06E': 98.5, '06B-III': 98.0, '06B-I': 46.6, '06A-III': 46.1, '06A-II': 45.1}",1,98.5,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007844935,"{'19F-I': 97.9, '19F': 97.2, '19F-III': 96.7, '19F-II': 95.2, '19F-IV': 90.3}",1,97.9,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001735965,"{'06E': 98.1, '06B-III': 97.9, '06B-I': 45.9, '06A-III': 45.3, '06A-II': 44.7}",1,98.1,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001344595,"{'31': 85.8, '41A': 53.4, '41F': 45.5, '06A-II': 35.9, '06A-VI': 35.9}",1,85.8,,31,,,{},{},31,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007786615,"{'01': 6.6, '45': 6.4, '25F': 5.8, '25A': 5.6, '22F': 5.3}",4,6.6,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901243205,"{'11D': 78.5, '11A': 77.2, '11F': 43.0, '11B': 32.5, '11C': 29.2}",1,78.5,,11A/11D,,,{},{},11A/11D,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007785165,"{'45': 6.4, '01': 6.3, '25F': 5.6, '25A': 5.4, '22F': 5.1}",3,6.4,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901250005,"{'06A': 93.5, '06A-III': 91.5, '06B-I': 91.4, '06B-II': 91.2, '06A-V': 90.7}",1,93.5,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(93.22)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907168575,"{'19A': 99.9, '19A-III': 99.7, '19A-I': 86.1, '19A-II': 83.6, '19AF': 57.1}",1,99.9,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(100.0)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907168165,"{'09A': 99.2, '09V': 99.0, '09N': 36.5, '09L': 35.0, '11F': 26.5}",1,99.2,,9A/9V,,,{},{},9A/9V,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_000944255,"{'10F': 98.2, '10C': 80.9, '10B': 22.4, '10A': 19.2, '20': 14.2}",1,98.2,,10F,,,{},{},10F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001329115,"{'19F-I': 95.9, '19F': 95.6, '19F-III': 94.0, '19F-II': 92.8, '19F-IV': 88.8}",1,95.9,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001336975,"{'31': 99.5, '41A': 57.3, '41F': 48.9, '06A-II': 36.4, '06A-VI': 36.4}",1,99.5,,31,,,{},{},31,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170485,"{'06E': 100.0, '06B-III': 99.4, '06B-I': 46.8, '06A-III': 46.3, '06A-II': 45.3}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001346275,"{'06A-IV': 2.3, '35B': 1.9, '38': 1.8, '45': 1.6, '09L': 1.5}",1,2.3,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001581375,"{'45': 6.5, '01': 6.0, '25F': 5.8, '25A': 5.6, '22F': 5.5}",3,6.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_002890075,"{'03': 95.1, '01': 17.8, '09N': 15.3, '09L': 15.2, '20': 15.2}",1,95.1,,3,,,{},{},3,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007786605,"{'01': 7.1, '45': 6.4, '25F': 5.8, '25A': 5.6, '22F': 5.2}",2,7.1,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170415,"{'23F': 99.4, '23A': 65.2, '28A': 47.8, '23B': 47.7, '06A-V': 45.6}",1,99.4,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001098865,"{'06C': 85.2, '06C-I': 85.2, '06D': 84.2, '06A': 76.9, '06A-IV': 73.3}",1,85.2,6A_6B_6C_6D,6A_6B_6C_6D,,[[0]],{'wciN': ['b: 83.5']},{'wciN': 0},6A_6B_6C_6D,RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007787645,"{'01': 7.3, '45': 6.4, '25F': 5.7, '25A': 5.5, '22F': 5.2}",3,7.3,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170205,"{'06B-I': 99.7, '06A-III': 97.6, '06B-II': 90.3, '06A': 89.8, '06A-V': 88.4}",1,99.7,6A_6B_6C_6D,6A_6B_6C_6D,,[[1]],"{'wciN': ['a', np.float64(100.0)]}",{'wciN': 'a'},6A/6B,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001339895,"{'23F': 94.0, '23A': 63.5, '28A': 48.5, '23B': 47.0, '06A': 46.2}",1,94.0,,23F,,,{},{},23F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001151845,"{'06D': 95.4, '06C': 87.5, '06C-I': 87.5, '06B-I': 75.6, '06A-III': 75.2}",1,95.4,6A_6B_6C_6D,6A_6B_6C_6D,,[[0]],{'wciN': ['b: 89.0']},{'wciN': 0},6A_6B_6C_6D,RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001144865,"{20: 0.3, 1: 0.1, 14: 0.1}",1,0.3,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901237925,"{'29': 88.2, '39': 20.9, '35F': 18.3, '22F': 16.9, '35B': 16.2}",1,88.2,,29,,,{},{},29,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901217925,"{'06E': 96.8, '06B-III': 95.1, '06B-I': 45.6, '06A-III': 45.0, '06A-IV': 44.3}",1,96.8,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(96.61)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001301855,"{'35F': 99.0, '47F': 74.3, '34': 26.7, '35B': 26.4, '29': 22.5}",1,99.0,,35F,,,{},{},35F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001337435,"{'35F': 53.5, '47F': 38.7, '35B': 23.8, '29': 22.2, '22F': 18.5}",1,53.5,,"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",,,{},{},"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907170205,"{'14': 92.5, '36': 28.0, '09L': 24.8, '15B': 24.2, '15C': 24.1}",1,92.5,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001130305,"{'06E': 100.0, '06B-III': 92.9, '06A-I': 42.2, '06B': 41.8, '06B-I': 40.9}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907171145,"{'14': 97.6, '36': 29.3, '09L': 25.9, '09N': 25.0, '15B': 24.2}",1,97.6,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001167265,"{'19F-I': 95.6, '19F': 95.3, '23F': 95.1, '19F-III': 93.8, '19F-II': 92.5}",1,95.6,,"Mixed serotypes- {'19F', '23F'}",,,{},{},"Mixed serotypes- {'19F', '23F'}",AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007784705,"{'01': 7.1, '25F': 6.1, '25A': 5.9, '36': 5.8, '38': 5.2}",3,7.1,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001142905,"{'19F-I': 97.1, '19F': 96.6, '19F-III': 96.4, '19F-II': 92.4, '19F-IV': 88.0}",1,97.1,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001107425,"{'15C': 87.7, '15B': 87.6, '15A': 64.5, '15F': 49.9, '23A': 30.2}",1,87.7,,15B/15C,,,{},{},15B/15C,AMBER
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007786565,"{'01': 7.4, '45': 6.4, '25F': 5.8, '25A': 5.6, '22F': 5.0}",5,7.4,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001857565,"{'19A-I': 98.4, '19A-II': 96.7, '19A': 87.1, '19A-III': 86.9, '19AF': 61.2}",1,98.4,19A_19AF,19A_19AF,,[[0]],{'wzy': ['1: 84.06']},{'wzy': 0},19A_19AF,RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_008039095,"{'45': 6.5, '01': 5.9, '25F': 5.8, '25A': 5.6, '22F': 5.2}",2,6.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001139565,"{'19F-I': 95.4, '19F': 95.2, '19F-III': 93.7, '19F-II': 92.3, '19F-IV': 88.3}",1,95.4,,19F,,,{},{},19F,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001101785,"{'06E': 100.0, '06B-III': 96.2, '06B-I': 43.6, '06A-III': 43.1, '06A-I': 42.6}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007785045,"{'01': 6.7, '45': 5.9, '25F': 5.7, '25A': 5.5, '22F': 5.3}",3,6.7,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_002866135,"{'45': 6.5, '01': 6.0, '25F': 5.8, '25A': 5.6, '22F': 5.2}",2,6.5,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_020038095,"{'15B': 64.4, '15C': 64.3, '19F': 58.2, '19F-I': 58.2, '19F-III': 57.3}",1,64.4,,"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",,,{},{},"Below 70% hit - Poor Sequence quality, variant or non-typeable organism.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_901247485,"{'19A-I': 99.4, '19A-II': 97.7, '19A': 88.0, '19A-III': 87.8, '19AF': 62.0}",1,99.4,19A_19AF,19A_19AF,,[[6]],"{'wzy': [1, np.float64(95.25)]}",{'wzy': 1},19A,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907167155,"{'09A': 99.7, '09V': 99.5, '09N': 36.2, '09L': 35.0, '11F': 26.6}",1,99.7,,9A/9V,,,{},{},9A/9V,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_900170655,"{'01': 6.3, '45': 5.5, '25F': 5.3, '20': 5.2, '25A': 5.1}",1,6.3,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_001146105,"{'06E': 100.0, '06B-III': 95.4, '06B-I': 42.7, '06A-I': 42.6, '06B': 42.2}",1,100.0,6A_6B_6C_6D,6A_6B_6C_6D,,[[3]],"{'wciN': ['g', np.float64(100.0)]}",{'wciN': 'g'},Serogroup_6_(6E),GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_907168215,"{'14': 93.4, '36': 27.0, '15B': 24.3, '15C': 24.2, '09L': 23.2}",1,93.4,,14,,,{},{},14,GREEN
sampleid,top_hits,max_mm,max_percent,folder,stage1_result,mix_mm,stage2_varids,stage2_hits,stage2_result,predicted_serotype,rag_status
GCA_007786865,"{'01': 7.2, '45': 6.4, '25F': 5.6, '25A': 5.4, '22F': 5.2}",3,7.2,,"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",,,{},{},"Below 20% hit - possible acapsular organism, check species identity and sequence quality.",RED