PrecisionFDA
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Explore HG002 comparison results
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| Entry | Type | Subtype | Subset | Genotype | F-score | Recall | Precision | Frac_NA | Truth TP | Truth FN | Query TP | Query FP | FP gt | % FP ma | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
62851-62900 / 86044 show all | |||||||||||||||
| ckim-gatk | INDEL | D6_15 | map_l100_m2_e1 | * | 95.6364 | 95.6364 | 95.6364 | 89.5556 | 263 | 12 | 263 | 12 | 2 | 16.6667 | |
| ckim-gatk | INDEL | D6_15 | map_l100_m2_e1 | het | 94.2446 | 97.0370 | 91.6084 | 92.2744 | 131 | 4 | 131 | 12 | 2 | 16.6667 | |
| ckim-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 96.6667 | 99.0244 | 94.4186 | 91.1777 | 203 | 2 | 203 | 12 | 11 | 91.6667 | |
| ckim-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 94.4009 | 91.5493 | 97.4359 | 75.4588 | 455 | 42 | 456 | 12 | 12 | 100.0000 | |
| ckim-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 96.6667 | 99.0244 | 94.4186 | 91.1777 | 203 | 2 | 203 | 12 | 11 | 91.6667 | |
| ckim-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.4398 | 100.0000 | 98.8858 | 68.4996 | 1065 | 0 | 1065 | 12 | 12 | 100.0000 | |
| ckim-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 94.2085 | 91.0448 | 97.6000 | 62.4906 | 488 | 48 | 488 | 12 | 10 | 83.3333 | |
| ckim-gatk | SNP | ti | map_siren | homalt | 91.8305 | 84.9219 | 99.9627 | 53.3585 | 32199 | 5717 | 32193 | 12 | 11 | 91.6667 | |
| ckim-gatk | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | * | 99.7116 | 99.6705 | 99.7527 | 66.7352 | 4840 | 16 | 4840 | 12 | 10 | 83.3333 | |
| ckim-isaac | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 78.4745 | 65.1883 | 98.5629 | 35.0700 | 779 | 416 | 823 | 12 | 11 | 91.6667 | |
| ckim-isaac | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 96.6320 | 94.0056 | 99.4094 | 36.1609 | 2023 | 129 | 2020 | 12 | 9 | 75.0000 | |
| ckim-dragen | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.7691 | 99.7171 | 99.8211 | 53.8271 | 6697 | 19 | 6696 | 12 | 7 | 58.3333 | |
| ckim-dragen | INDEL | D6_15 | HG002complexvar | het | 99.2569 | 98.9103 | 99.6060 | 59.0976 | 3086 | 34 | 3034 | 12 | 10 | 83.3333 | |
| ckim-dragen | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 96.6667 | 99.0244 | 94.4186 | 90.8276 | 203 | 2 | 203 | 12 | 11 | 91.6667 | |
| ckim-dragen | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 96.8266 | 95.4876 | 98.2036 | 81.6484 | 656 | 31 | 656 | 12 | 10 | 83.3333 | |
| ckim-dragen | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 96.6667 | 99.0244 | 94.4186 | 90.8276 | 203 | 2 | 203 | 12 | 11 | 91.6667 | |
| ckim-dragen | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.7238 | 91.2679 | 98.4516 | 67.1749 | 763 | 73 | 763 | 12 | 11 | 91.6667 | |
| ckim-dragen | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.5612 | 97.7676 | 99.3678 | 76.3607 | 1927 | 44 | 1886 | 12 | 6 | 50.0000 | |
| ckim-dragen | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.5612 | 97.7676 | 99.3678 | 76.3607 | 1927 | 44 | 1886 | 12 | 6 | 50.0000 | |
| cchapple-custom | INDEL | C1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 0.0000 | 0.0000 | 61.2903 | 93.6214 | 0 | 0 | 19 | 12 | 2 | 16.6667 | |
| cchapple-custom | INDEL | C1_5 | map_l100_m0_e0 | * | 0.0000 | 0.0000 | 57.1429 | 94.9091 | 0 | 0 | 16 | 12 | 5 | 41.6667 | |
| cchapple-custom | INDEL | C1_5 | map_l100_m0_e0 | het | 0.0000 | 0.0000 | 45.4545 | 94.8598 | 0 | 0 | 10 | 12 | 5 | 41.6667 | |
| cchapple-custom | INDEL | D16_PLUS | map_l100_m1_e0 | het | 84.8574 | 86.9565 | 82.8571 | 91.8320 | 40 | 6 | 58 | 12 | 7 | 58.3333 | |
| cchapple-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 96.7502 | 94.8052 | 98.7768 | 42.3619 | 365 | 20 | 969 | 12 | 7 | 58.3333 | |
| cchapple-custom | INDEL | I16_PLUS | HG002complexvar | homalt | 98.0066 | 100.0000 | 96.0912 | 61.8634 | 309 | 0 | 295 | 12 | 11 | 91.6667 | |
| gduggal-snapplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 50.0000 | 39.1304 | 69.2308 | 97.4017 | 27 | 42 | 27 | 12 | 6 | 50.0000 | |
| gduggal-snapplat | SNP | ti | map_l100_m1_e0 | homalt | 96.1786 | 92.7004 | 99.9279 | 60.1160 | 16649 | 1311 | 16632 | 12 | 12 | 100.0000 | |
| gduggal-snapplat | SNP | tv | HG002complexvar | hetalt | 91.0113 | 86.7742 | 95.6835 | 42.9158 | 269 | 41 | 266 | 12 | 12 | 100.0000 | |
| gduggal-snapvard | INDEL | C1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 0.0000 | 0.0000 | 60.0000 | 94.2857 | 0 | 0 | 18 | 12 | 4 | 33.3333 | |
| gduggal-snapvard | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 76.8743 | 65.1163 | 93.8144 | 55.2995 | 168 | 90 | 182 | 12 | 10 | 83.3333 | |
| gduggal-snapfb | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | hetalt | 14.2857 | 100.0000 | 7.6923 | 60.6061 | 1 | 0 | 1 | 12 | 0 | 0.0000 | |
| gduggal-snapfb | SNP | tv | map_l250_m2_e0 | homalt | 95.9430 | 93.3831 | 98.6471 | 93.4664 | 875 | 62 | 875 | 12 | 5 | 41.6667 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 21.9561 | 12.5000 | 90.1639 | 55.1471 | 109 | 763 | 110 | 12 | 10 | 83.3333 | |
| gduggal-snapplat | INDEL | I1_5 | map_l100_m0_e0 | homalt | 86.6295 | 80.7692 | 93.4066 | 89.1538 | 168 | 40 | 170 | 12 | 1 | 8.3333 | |
| gduggal-snapplat | INDEL | I1_5 | map_l250_m1_e0 | het | 72.5664 | 68.3333 | 77.3585 | 98.6126 | 41 | 19 | 41 | 12 | 0 | 0.0000 | |
| gduggal-snapplat | INDEL | I1_5 | map_l250_m2_e0 | het | 74.1935 | 69.6970 | 79.3103 | 98.6878 | 46 | 20 | 46 | 12 | 0 | 0.0000 | |
| gduggal-snapplat | INDEL | I1_5 | map_l250_m2_e1 | het | 74.1935 | 69.6970 | 79.3103 | 98.7342 | 46 | 20 | 46 | 12 | 0 | 0.0000 | |
| gduggal-snapplat | INDEL | I1_5 | map_siren | hetalt | 38.7454 | 26.7857 | 70.0000 | 97.4795 | 30 | 82 | 28 | 12 | 6 | 50.0000 | |
| gduggal-snapplat | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 27.7325 | 18.4783 | 55.5556 | 75.0000 | 17 | 75 | 15 | 12 | 4 | 33.3333 | |
| gduggal-snapplat | INDEL | I6_15 | segdup | het | 37.0075 | 26.5060 | 61.2903 | 95.4210 | 22 | 61 | 19 | 12 | 1 | 8.3333 | |
| gduggal-snapplat | SNP | * | HG002complexvar | hetalt | 91.0113 | 86.7742 | 95.6835 | 42.9158 | 269 | 41 | 266 | 12 | 12 | 100.0000 | |
| gduggal-snapvard | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 98.1212 | 96.7368 | 99.5458 | 35.0221 | 2668 | 90 | 2630 | 12 | 9 | 75.0000 | |
| gduggal-snapvard | SNP | tv | map_l125_m2_e0 | homalt | 98.0723 | 96.4102 | 99.7927 | 68.8173 | 5801 | 216 | 5778 | 12 | 9 | 75.0000 | |
| gduggal-snapvard | SNP | tv | map_l125_m2_e1 | homalt | 98.0309 | 96.3286 | 99.7943 | 68.8883 | 5851 | 223 | 5823 | 12 | 9 | 75.0000 | |
| ghariani-varprowl | INDEL | D6_15 | map_l150_m1_e0 | * | 81.9444 | 80.8219 | 83.0986 | 93.6036 | 59 | 14 | 59 | 12 | 11 | 91.6667 | |
| ghariani-varprowl | INDEL | D6_15 | map_l150_m1_e0 | het | 86.6667 | 100.0000 | 76.4706 | 94.7639 | 39 | 0 | 39 | 12 | 11 | 91.6667 | |
| ghariani-varprowl | INDEL | D6_15 | map_l150_m2_e0 | * | 83.2298 | 81.7073 | 84.8101 | 93.6342 | 67 | 15 | 67 | 12 | 11 | 91.6667 | |
| ghariani-varprowl | INDEL | D6_15 | map_l150_m2_e0 | het | 87.3786 | 97.8261 | 78.9474 | 94.7368 | 45 | 1 | 45 | 12 | 11 | 91.6667 | |
| ghariani-varprowl | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 84.9558 | 90.5660 | 80.0000 | 72.3502 | 48 | 5 | 48 | 12 | 12 | 100.0000 | |
| ghariani-varprowl | INDEL | I1_5 | map_l150_m0_e0 | het | 93.6937 | 98.1132 | 89.6552 | 95.7571 | 104 | 2 | 104 | 12 | 3 | 25.0000 | |