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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
43151-43200 / 86044 show all | |||||||||||||||
| cchapple-custom | INDEL | D16_PLUS | map_l125_m2_e1 | * | 89.6552 | 92.8571 | 86.6667 | 95.3125 | 26 | 2 | 26 | 4 | 0 | 0.0000 | |
| cchapple-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_51to200 | homalt | 92.8571 | 100.0000 | 86.6667 | 40.0000 | 13 | 0 | 13 | 2 | 2 | 100.0000 | |
| cchapple-custom | INDEL | I16_PLUS | map_l100_m1_e0 | * | 91.1641 | 96.1538 | 86.6667 | 93.9880 | 25 | 1 | 26 | 4 | 1 | 25.0000 | |
| cchapple-custom | INDEL | I16_PLUS | map_l100_m2_e0 | * | 91.1641 | 96.1538 | 86.6667 | 94.7826 | 25 | 1 | 26 | 4 | 1 | 25.0000 | |
| cchapple-custom | INDEL | I16_PLUS | map_l100_m2_e1 | * | 91.1641 | 96.1538 | 86.6667 | 94.8718 | 25 | 1 | 26 | 4 | 1 | 25.0000 | |
| ckim-gatk | INDEL | D1_5 | map_l250_m2_e1 | * | 92.1519 | 98.3784 | 86.6667 | 96.9213 | 182 | 3 | 182 | 28 | 1 | 3.5714 | |
| ckim-gatk | INDEL | I6_15 | map_l125_m0_e0 | * | 86.6667 | 86.6667 | 86.6667 | 96.0212 | 13 | 2 | 13 | 2 | 1 | 50.0000 | |
| gduggal-snapvard | SNP | * | map_l125_m2_e1 | het | 91.4989 | 96.9163 | 86.6551 | 82.4293 | 28726 | 914 | 28383 | 4371 | 310 | 7.0922 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 88.8749 | 91.2134 | 86.6534 | 76.1180 | 436 | 42 | 435 | 67 | 12 | 17.9104 | |
| ghariani-varprowl | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 85.8567 | 85.0746 | 86.6532 | 64.3732 | 855 | 150 | 857 | 132 | 126 | 95.4545 | |
| jpowers-varprowl | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 84.4600 | 82.3881 | 86.6388 | 62.5342 | 828 | 177 | 830 | 128 | 125 | 97.6562 | |
| gduggal-snapplat | INDEL | I1_5 | map_l125_m2_e1 | het | 82.6084 | 78.9370 | 86.6379 | 94.9067 | 401 | 107 | 402 | 62 | 3 | 4.8387 | |
| gduggal-snapplat | INDEL | D1_5 | map_l150_m2_e0 | het | 83.8926 | 81.3230 | 86.6300 | 94.6747 | 418 | 96 | 473 | 73 | 17 | 23.2877 | |
| gduggal-snapvard | INDEL | I1_5 | map_l125_m2_e0 | * | 90.3981 | 94.5158 | 86.6242 | 88.6067 | 810 | 47 | 1088 | 168 | 70 | 41.6667 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 91.0906 | 96.0483 | 86.6196 | 46.4616 | 2625 | 108 | 7477 | 1155 | 540 | 46.7532 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 87.7794 | 88.9764 | 86.6142 | 67.2680 | 113 | 14 | 110 | 17 | 11 | 64.7059 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 89.1434 | 91.8292 | 86.6102 | 71.1229 | 3248 | 289 | 20162 | 3117 | 3094 | 99.2621 | |
| ckim-isaac | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 82.6787 | 79.0895 | 86.6092 | 82.6495 | 1025 | 271 | 1106 | 171 | 82 | 47.9532 | |
| qzeng-custom | INDEL | D6_15 | segdup | * | 89.7775 | 93.1937 | 86.6029 | 93.7519 | 178 | 13 | 181 | 28 | 9 | 32.1429 | |
| ckim-gatk | INDEL | D1_5 | map_l250_m2_e0 | * | 92.1120 | 98.3696 | 86.6029 | 96.8600 | 181 | 3 | 181 | 28 | 1 | 3.5714 | |
| gduggal-bwavard | INDEL | D1_5 | map_l100_m1_e0 | het | 92.3518 | 98.9247 | 86.5979 | 88.3812 | 1196 | 13 | 1176 | 182 | 48 | 26.3736 | |
| gduggal-snapplat | INDEL | D1_5 | map_l150_m2_e1 | het | 83.7221 | 81.0345 | 86.5942 | 94.7283 | 423 | 99 | 478 | 74 | 17 | 22.9730 | |
| gduggal-snapplat | INDEL | I1_5 | map_l125_m2_e0 | het | 82.6633 | 79.0744 | 86.5934 | 94.8547 | 393 | 104 | 394 | 61 | 3 | 4.9180 | |
| gduggal-snapvard | SNP | * | map_l125_m2_e0 | het | 91.4436 | 96.8927 | 86.5748 | 82.3864 | 28407 | 911 | 28071 | 4353 | 308 | 7.0756 | |
| anovak-vg | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 88.3047 | 90.1065 | 86.5734 | 76.6949 | 592 | 65 | 619 | 96 | 50 | 52.0833 | |
| qzeng-custom | INDEL | D6_15 | map_l150_m2_e0 | het | 83.3884 | 80.4348 | 86.5672 | 94.7368 | 37 | 9 | 58 | 9 | 3 | 33.3333 | |
| qzeng-custom | INDEL | D6_15 | map_l150_m2_e1 | het | 83.6115 | 80.8511 | 86.5672 | 94.8102 | 38 | 9 | 58 | 9 | 3 | 33.3333 | |
| raldana-dualsentieon | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 92.0635 | 98.3051 | 86.5672 | 75.1852 | 58 | 1 | 58 | 9 | 9 | 100.0000 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | * | 75.9280 | 67.6190 | 86.5649 | 44.3027 | 497 | 238 | 567 | 88 | 88 | 100.0000 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 56.1615 | 41.5637 | 86.5642 | 60.9124 | 3397 | 4776 | 3434 | 533 | 458 | 85.9287 | |
| ndellapenna-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 85.7255 | 84.9037 | 86.5634 | 80.2326 | 36793 | 6542 | 37456 | 5814 | 5159 | 88.7341 | |
| gduggal-snapplat | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 25.0124 | 14.6182 | 86.5625 | 67.4300 | 559 | 3265 | 554 | 86 | 66 | 76.7442 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 91.0757 | 96.0870 | 86.5613 | 76.5524 | 221 | 9 | 219 | 34 | 27 | 79.4118 | |
| qzeng-custom | INDEL | * | HG002compoundhet | het | 90.0667 | 93.8691 | 86.5604 | 55.7571 | 3843 | 251 | 30091 | 4672 | 2782 | 59.5462 | |
| egarrison-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 85.6704 | 84.8021 | 86.5567 | 80.2451 | 36749 | 6586 | 37209 | 5779 | 5249 | 90.8289 | |
| anovak-vg | INDEL | D1_5 | map_siren | * | 87.4723 | 88.4103 | 86.5539 | 80.0641 | 3120 | 409 | 3122 | 485 | 188 | 38.7629 | |
| asubramanian-gatk | INDEL | D1_5 | map_l250_m1_e0 | * | 86.5497 | 86.5497 | 86.5497 | 96.4640 | 148 | 23 | 148 | 23 | 2 | 8.6957 | |
| qzeng-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 84.4697 | 82.4873 | 86.5497 | 58.4519 | 975 | 207 | 1036 | 161 | 135 | 83.8509 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 80.0676 | 74.4893 | 86.5491 | 57.6750 | 13163 | 4508 | 13345 | 2074 | 1774 | 85.5352 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 80.0676 | 74.4893 | 86.5491 | 57.6750 | 13163 | 4508 | 13345 | 2074 | 1774 | 85.5352 | |
| gduggal-snapplat | INDEL | I1_5 | map_l125_m1_e0 | het | 82.7206 | 79.2181 | 86.5471 | 94.3473 | 385 | 101 | 386 | 60 | 3 | 5.0000 | |
| mlin-fermikit | SNP | ti | map_l150_m1_e0 | * | 56.8574 | 42.3346 | 86.5470 | 60.8408 | 8345 | 11367 | 8344 | 1297 | 1150 | 88.6662 | |
| gduggal-snapplat | INDEL | * | map_l100_m0_e0 | het | 80.0362 | 74.4368 | 86.5466 | 93.5607 | 760 | 261 | 817 | 127 | 18 | 14.1732 | |
| qzeng-custom | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | homalt | 89.9387 | 93.6170 | 86.5385 | 51.8519 | 44 | 3 | 45 | 7 | 7 | 100.0000 | |
| eyeh-varpipe | INDEL | I16_PLUS | HG002complexvar | hetalt | 21.9016 | 12.5373 | 86.5385 | 70.1149 | 42 | 293 | 45 | 7 | 7 | 100.0000 | |
| jlack-gatk | INDEL | D6_15 | map_l150_m2_e0 | het | 91.8367 | 97.8261 | 86.5385 | 95.0617 | 45 | 1 | 45 | 7 | 0 | 0.0000 | |
| mlin-fermikit | SNP | tv | map_siren | homalt | 81.9952 | 77.9060 | 86.5373 | 48.2163 | 13431 | 3809 | 13428 | 2089 | 1999 | 95.6917 | |
| mlin-fermikit | INDEL | D1_5 | map_siren | homalt | 85.9425 | 85.3596 | 86.5334 | 78.1760 | 997 | 171 | 996 | 155 | 149 | 96.1290 | |
| cchapple-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 91.1652 | 96.3415 | 86.5169 | 61.6379 | 79 | 3 | 77 | 12 | 12 | 100.0000 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 90.3274 | 94.4904 | 86.5158 | 75.9742 | 2058 | 120 | 1835 | 286 | 264 | 92.3077 | |