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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
68901-68950 / 86044 show all | |||||||||||||||
| ckim-vqsr | INDEL | D6_15 | HG002compoundhet | hetalt | 96.9271 | 94.4179 | 99.5733 | 24.1268 | 7696 | 455 | 7700 | 33 | 33 | 100.0000 | |
| ckim-isaac | INDEL | D16_PLUS | HG002complexvar | hetalt | 71.9738 | 58.7045 | 92.9936 | 55.5660 | 145 | 102 | 438 | 33 | 26 | 78.7879 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 94.0932 | 92.0824 | 96.1938 | 68.2998 | 849 | 73 | 834 | 33 | 15 | 45.4545 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 93.8012 | 88.8400 | 99.3492 | 39.7743 | 5047 | 634 | 5038 | 33 | 25 | 75.7576 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 94.2777 | 89.5819 | 99.4931 | 26.8704 | 6492 | 755 | 6477 | 33 | 25 | 75.7576 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 81.7466 | 69.7674 | 98.6920 | 34.2284 | 2460 | 1066 | 2490 | 33 | 24 | 72.7273 | |
| egarrison-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 72.9624 | 58.1711 | 97.8403 | 43.0063 | 1584 | 1139 | 1495 | 33 | 31 | 93.9394 | |
| dgrover-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.2368 | 99.3209 | 97.1761 | 73.3746 | 1170 | 8 | 1170 | 34 | 34 | 100.0000 | |
| ckim-isaac | SNP | ti | map_l125_m2_e0 | het | 78.5719 | 64.8231 | 99.7229 | 74.9990 | 12236 | 6640 | 12236 | 34 | 3 | 8.8235 | |
| ckim-isaac | SNP | ti | map_l125_m2_e1 | het | 78.6508 | 64.9290 | 99.7264 | 75.0040 | 12393 | 6694 | 12393 | 34 | 3 | 8.8235 | |
| ckim-isaac | SNP | tv | map_l100_m2_e1 | het | 79.3382 | 65.8928 | 99.6774 | 69.5352 | 10502 | 5436 | 10505 | 34 | 8 | 23.5294 | |
| ckim-vqsr | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.5715 | 99.4508 | 99.6924 | 63.7612 | 11047 | 61 | 11021 | 34 | 16 | 47.0588 | |
| ckim-vqsr | SNP | ti | map_l250_m2_e1 | * | 59.7117 | 42.8487 | 98.4608 | 97.0448 | 2175 | 2901 | 2175 | 34 | 0 | 0.0000 | |
| ckim-vqsr | SNP | ti | map_l250_m2_e1 | het | 69.7793 | 54.1376 | 98.1319 | 97.0902 | 1786 | 1513 | 1786 | 34 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.4972 | 95.5852 | 99.4871 | 26.0156 | 6582 | 304 | 6595 | 34 | 33 | 97.0588 | |
| dgrover-gatk | INDEL | D6_15 | HG002compoundhet | hetalt | 97.2251 | 94.9945 | 99.5630 | 24.6392 | 7743 | 408 | 7747 | 34 | 33 | 97.0588 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 82.5301 | 85.0932 | 80.1170 | 31.8725 | 137 | 24 | 137 | 34 | 15 | 44.1176 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 98.0651 | 97.0076 | 99.1459 | 33.5614 | 3955 | 122 | 3947 | 34 | 24 | 70.5882 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 90.7836 | 84.1298 | 98.5804 | 37.3201 | 2359 | 445 | 2361 | 34 | 27 | 79.4118 | |
| ckim-isaac | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 70.1173 | 56.6230 | 92.0561 | 70.3396 | 389 | 298 | 394 | 34 | 20 | 58.8235 | |
| ckim-isaac | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 66.5163 | 53.3333 | 88.3562 | 71.0030 | 256 | 224 | 258 | 34 | 20 | 58.8235 | |
| ckim-isaac | INDEL | I6_15 | HG002compoundhet | hetalt | 82.1207 | 69.9426 | 99.4336 | 21.1377 | 5971 | 2566 | 5969 | 34 | 23 | 67.6471 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 90.8228 | 92.2830 | 89.4081 | 69.5735 | 287 | 24 | 287 | 34 | 29 | 85.2941 | |
| egarrison-hhga | SNP | * | map_l250_m2_e0 | * | 98.7146 | 97.8821 | 99.5614 | 88.2472 | 7718 | 167 | 7718 | 34 | 16 | 47.0588 | |
| egarrison-hhga | SNP | * | map_l250_m2_e1 | * | 98.7184 | 97.8841 | 99.5670 | 88.3214 | 7818 | 169 | 7818 | 34 | 16 | 47.0588 | |
| egarrison-hhga | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.3832 | 99.0868 | 99.6813 | 36.6712 | 10634 | 98 | 10635 | 34 | 19 | 55.8824 | |
| egarrison-hhga | SNP | ti | map_l150_m1_e0 | het | 99.1299 | 98.5449 | 99.7219 | 75.0856 | 12190 | 180 | 12190 | 34 | 13 | 38.2353 | |
| egarrison-hhga | SNP | ti | map_l150_m2_e0 | het | 99.1606 | 98.5948 | 99.7330 | 76.2545 | 12700 | 181 | 12700 | 34 | 13 | 38.2353 | |
| egarrison-hhga | SNP | tv | map_l125_m1_e0 | * | 99.3983 | 99.0135 | 99.7861 | 68.1855 | 15858 | 158 | 15858 | 34 | 17 | 50.0000 | |
| eyeh-varpipe | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | het | 71.1860 | 58.6207 | 90.6077 | 99.6597 | 51 | 36 | 328 | 34 | 30 | 88.2353 | |
| eyeh-varpipe | INDEL | * | map_l125_m1_e0 | homalt | 97.0129 | 97.1311 | 96.8950 | 86.7449 | 711 | 21 | 1061 | 34 | 31 | 91.1765 | |
| eyeh-varpipe | INDEL | C1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 0.0000 | 0.0000 | 24.4444 | 96.6518 | 0 | 0 | 11 | 34 | 22 | 64.7059 | |
| ckim-vqsr | SNP | * | HG002compoundhet | het | 99.1735 | 98.5964 | 99.7573 | 46.7768 | 13979 | 199 | 13977 | 34 | 25 | 73.5294 | |
| ndellapenna-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 98.9791 | 99.2182 | 98.7412 | 58.5355 | 2665 | 21 | 2667 | 34 | 4 | 11.7647 | |
| ndellapenna-hhga | SNP | * | map_l250_m1_e0 | * | 98.0684 | 96.6630 | 99.5153 | 86.9145 | 6981 | 241 | 6981 | 34 | 19 | 55.8824 | |
| ndellapenna-hhga | SNP | * | map_siren | homalt | 99.8258 | 99.7135 | 99.9382 | 52.6378 | 54998 | 158 | 54999 | 34 | 30 | 88.2353 | |
| ndellapenna-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 92.2021 | 88.9542 | 95.6962 | 86.1888 | 757 | 94 | 756 | 34 | 14 | 41.1765 | |
| ndellapenna-hhga | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 97.8068 | 96.9376 | 98.6918 | 81.5857 | 2564 | 81 | 2565 | 34 | 13 | 38.2353 | |
| qzeng-custom | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 90.4993 | 83.4558 | 98.8412 | 37.5745 | 8742 | 1733 | 2900 | 34 | 26 | 76.4706 | |
| qzeng-custom | INDEL | * | map_l250_m2_e0 | * | 75.8372 | 65.8610 | 89.3750 | 97.9118 | 218 | 113 | 286 | 34 | 17 | 50.0000 | |
| 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 | |
| ndellapenna-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 96.7182 | 95.3340 | 98.1431 | 70.1548 | 1798 | 88 | 1797 | 34 | 22 | 64.7059 | |
| ndellapenna-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 73.6158 | 59.0525 | 97.7135 | 42.8517 | 1608 | 1115 | 1453 | 34 | 29 | 85.2941 | |
| ndellapenna-hhga | INDEL | * | map_l125_m1_e0 | het | 97.3464 | 97.2285 | 97.4646 | 85.8260 | 1298 | 37 | 1307 | 34 | 9 | 26.4706 | |
| ndellapenna-hhga | INDEL | * | map_l125_m2_e0 | het | 97.4161 | 97.2682 | 97.5645 | 86.6946 | 1353 | 38 | 1362 | 34 | 9 | 26.4706 | |
| ndellapenna-hhga | INDEL | * | map_l125_m2_e1 | het | 97.4472 | 97.3011 | 97.5938 | 86.8092 | 1370 | 38 | 1379 | 34 | 9 | 26.4706 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 94.9898 | 94.4882 | 95.4967 | 65.8834 | 720 | 42 | 721 | 34 | 23 | 67.6471 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 63.9253 | 47.2441 | 98.8157 | 36.3273 | 3360 | 3752 | 2837 | 34 | 29 | 85.2941 | |
| qzeng-custom | SNP | ti | func_cds | het | 99.7296 | 99.8589 | 99.6007 | 30.7386 | 8492 | 12 | 8481 | 34 | 1 | 2.9412 | |
| qzeng-custom | SNP | tv | map_l150_m2_e0 | homalt | 81.9655 | 70.0220 | 98.8211 | 73.9641 | 2859 | 1224 | 2850 | 34 | 34 | 100.0000 | |