PrecisionFDA
Truth Challenge
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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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
71451-71500 / 86044 show all | |||||||||||||||
| gduggal-snapplat | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 0.0000 | 0.0000 | 0.0000 | 0 | 133 | 0 | 0 | 0 | |||
| gduggal-snapplat | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 40.3615 | 29.2553 | 65.0602 | 70.8772 | 55 | 133 | 54 | 29 | 19 | 65.5172 | |
| gduggal-snapvard | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 0.0000 | 0.0000 | 28.4211 | 61.3821 | 0 | 133 | 27 | 68 | 23 | 33.8235 | |
| gduggal-snapvard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 75.6451 | 61.5607 | 98.0861 | 70.4802 | 213 | 133 | 205 | 4 | 4 | 100.0000 | |
| gduggal-snapfb | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 0.0000 | 0.0000 | 0.0000 | 0 | 133 | 0 | 0 | 0 | |||
| ghariani-varprowl | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 88.9998 | 98.0021 | 81.5123 | 84.1232 | 6524 | 133 | 6565 | 1489 | 141 | 9.4694 | |
| ndellapenna-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.3248 | 99.2165 | 99.4333 | 71.0574 | 16842 | 133 | 16845 | 96 | 85 | 88.5417 | |
| ndellapenna-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.3248 | 99.2165 | 99.4333 | 71.0574 | 16842 | 133 | 16845 | 96 | 85 | 88.5417 | |
| mlin-fermikit | INDEL | * | segdup | * | 95.7518 | 94.7966 | 96.7265 | 92.3178 | 2423 | 133 | 2423 | 82 | 67 | 81.7073 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 83.8170 | 96.5624 | 74.0438 | 56.3581 | 3736 | 133 | 4259 | 1493 | 1471 | 98.5265 | |
| dgrover-gatk | INDEL | D16_PLUS | * | * | 97.8781 | 98.0395 | 97.7172 | 70.6733 | 6651 | 133 | 6635 | 155 | 103 | 66.4516 | |
| egarrison-hhga | SNP | tv | map_l150_m2_e0 | * | 99.2922 | 98.8287 | 99.7600 | 74.2574 | 11222 | 133 | 11222 | 27 | 12 | 44.4444 | |
| egarrison-hhga | SNP | tv | map_l150_m2_e1 | * | 99.3012 | 98.8437 | 99.7631 | 74.2719 | 11369 | 133 | 11369 | 27 | 12 | 44.4444 | |
| rpoplin-dv42 | SNP | ti | map_l150_m0_e0 | * | 98.6405 | 98.3081 | 98.9751 | 78.2174 | 7728 | 133 | 7726 | 80 | 57 | 71.2500 | |
| rpoplin-dv42 | SNP | tv | map_l150_m2_e0 | * | 98.9506 | 98.8287 | 99.0728 | 74.8529 | 11222 | 133 | 11220 | 105 | 61 | 58.0952 | |
| rpoplin-dv42 | SNP | tv | map_l150_m2_e1 | * | 98.9641 | 98.8437 | 99.0847 | 74.8658 | 11369 | 133 | 11367 | 105 | 61 | 58.0952 | |
| hfeng-pmm1 | INDEL | I1_5 | * | homalt | 99.7725 | 99.7799 | 99.7651 | 52.5960 | 60295 | 133 | 60299 | 142 | 137 | 96.4789 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 91.8593 | 86.7265 | 97.6378 | 63.9497 | 869 | 133 | 868 | 21 | 15 | 71.4286 | |
| jlack-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.2940 | 99.3207 | 97.2884 | 75.8975 | 19446 | 133 | 19446 | 542 | 30 | 5.5351 | |
| jlack-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.2940 | 99.3207 | 97.2884 | 75.8975 | 19446 | 133 | 19446 | 542 | 30 | 5.5351 | |
| hfeng-pmm2 | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.5395 | 97.2611 | 99.8520 | 63.6434 | 4723 | 133 | 4723 | 7 | 5 | 71.4286 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.3527 | 98.8800 | 99.8300 | 48.5551 | 11742 | 133 | 11747 | 20 | 11 | 55.0000 | |
| hfeng-pmm3 | SNP | tv | map_siren | * | 99.7604 | 99.7104 | 99.8104 | 56.7354 | 45797 | 133 | 45789 | 87 | 15 | 17.2414 | |
| hfeng-pmm3 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 97.2324 | 94.9716 | 99.6035 | 82.0153 | 2512 | 133 | 2512 | 10 | 3 | 30.0000 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 76.5432 | 62.0000 | 100.0000 | 30.8176 | 217 | 133 | 110 | 0 | 0 | ||
| eyeh-varpipe | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 74.2076 | 65.4545 | 85.6631 | 71.8750 | 252 | 133 | 239 | 40 | 3 | 7.5000 | |
| gduggal-bwavard | SNP | ti | map_l150_m0_e0 | het | 90.2624 | 97.3906 | 84.1064 | 88.1487 | 4964 | 133 | 4932 | 932 | 44 | 4.7210 | |
| gduggal-snapfb | INDEL | * | segdup | het | 92.4787 | 90.9277 | 94.0836 | 94.1056 | 1333 | 133 | 1463 | 92 | 26 | 28.2609 | |
| gduggal-bwavard | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 93.8459 | 95.8744 | 91.9015 | 78.3452 | 3114 | 134 | 3098 | 273 | 32 | 11.7216 | |
| gduggal-bwavard | SNP | tv | map_l100_m0_e0 | het | 91.6040 | 98.1446 | 85.8808 | 81.9878 | 7088 | 134 | 7074 | 1163 | 45 | 3.8693 | |
| mlin-fermikit | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 94.9292 | 96.3368 | 93.5621 | 42.6632 | 3524 | 134 | 3517 | 242 | 235 | 97.1074 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 98.5228 | 97.5359 | 99.5300 | 31.9212 | 5304 | 134 | 5294 | 25 | 25 | 100.0000 | |
| ltrigg-rtg2 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 87.9958 | 80.4949 | 97.0383 | 67.7165 | 553 | 134 | 557 | 17 | 15 | 88.2353 | |
| ltrigg-rtg2 | SNP | * | map_siren | homalt | 99.8557 | 99.7571 | 99.9546 | 50.5157 | 55022 | 134 | 55010 | 25 | 22 | 88.0000 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 90.5530 | 86.6267 | 94.8521 | 57.6727 | 868 | 134 | 866 | 47 | 35 | 74.4681 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 25.1397 | 100.0000 | 45 | 134 | 0 | 0 | 0 | ||||
| mlin-fermikit | SNP | * | func_cds | * | 99.4453 | 99.2617 | 99.6295 | 19.0809 | 18016 | 134 | 18016 | 67 | 48 | 71.6418 | |
| ckim-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 96.7765 | 93.8813 | 99.8559 | 30.0168 | 2056 | 134 | 2079 | 3 | 3 | 100.0000 | |
| ckim-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 95.9847 | 92.4337 | 99.8195 | 35.5314 | 1637 | 134 | 1659 | 3 | 3 | 100.0000 | |
| cchapple-custom | SNP | tv | map_l150_m2_e0 | homalt | 98.3317 | 96.7181 | 100.0000 | 69.7502 | 3949 | 134 | 3947 | 0 | 0 | ||
| cchapple-custom | SNP | tv | map_l150_m2_e1 | homalt | 98.3526 | 96.7586 | 100.0000 | 69.7328 | 4000 | 134 | 3998 | 0 | 0 | ||
| cchapple-custom | INDEL | * | map_l100_m2_e1 | * | 95.9700 | 96.4324 | 95.5120 | 84.7746 | 3622 | 134 | 3703 | 174 | 52 | 29.8851 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 73.1064 | 82.4147 | 65.6873 | 70.7937 | 628 | 134 | 626 | 327 | 81 | 24.7706 | |
| astatham-gatk | SNP | * | map_l150_m1_e0 | homalt | 99.3312 | 98.8113 | 99.8566 | 68.4753 | 11139 | 134 | 11139 | 16 | 13 | 81.2500 | |
| bgallagher-sentieon | SNP | ti | map_l150_m1_e0 | * | 99.1792 | 99.3202 | 99.0387 | 75.5864 | 19578 | 134 | 19574 | 190 | 36 | 18.9474 | |
| bgallagher-sentieon | SNP | tv | map_siren | * | 99.5565 | 99.7083 | 99.4051 | 58.5993 | 45796 | 134 | 45788 | 274 | 36 | 13.1387 | |
| jpowers-varprowl | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 67.9363 | 62.1469 | 74.9153 | 66.2471 | 220 | 134 | 221 | 74 | 74 | 100.0000 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 96.0152 | 93.7848 | 98.3543 | 70.3629 | 2022 | 134 | 2032 | 34 | 5 | 14.7059 | |
| jmaeng-gatk | INDEL | D16_PLUS | HG002compoundhet | hetalt | 96.2053 | 93.0498 | 99.5822 | 25.8327 | 1794 | 134 | 1907 | 8 | 8 | 100.0000 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 99.1151 | 98.3983 | 99.8425 | 40.4315 | 8232 | 134 | 8242 | 13 | 12 | 92.3077 | |