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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
26001-26050 / 86044 show all | |||||||||||||||
| dgrover-gatk | INDEL | * | map_l125_m0_e0 | * | 97.4564 | 97.6190 | 97.2943 | 90.7643 | 861 | 21 | 863 | 24 | 6 | 25.0000 | |
| dgrover-gatk | INDEL | * | segdup | * | 99.0625 | 99.1784 | 98.9470 | 94.7737 | 2535 | 21 | 2537 | 27 | 10 | 37.0370 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 99.1916 | 98.5934 | 99.7970 | 32.9401 | 1472 | 21 | 1475 | 3 | 3 | 100.0000 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | * | 96.8147 | 96.5909 | 97.0395 | 67.8647 | 595 | 21 | 590 | 18 | 16 | 88.8889 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.9511 | 97.2441 | 98.6684 | 67.2767 | 741 | 21 | 741 | 10 | 7 | 70.0000 | |
| ckim-vqsr | INDEL | D1_5 | map_l150_m1_e0 | het | 94.8621 | 95.6432 | 94.0937 | 93.3890 | 461 | 21 | 462 | 29 | 3 | 10.3448 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 92.2217 | 96.5630 | 88.2540 | 72.0249 | 590 | 21 | 556 | 74 | 70 | 94.5946 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.2282 | 99.3586 | 97.1232 | 68.6872 | 3253 | 21 | 3241 | 96 | 93 | 96.8750 | |
| ckim-vqsr | INDEL | I1_5 | map_l150_m1_e0 | het | 94.7247 | 92.9766 | 96.5398 | 94.1248 | 278 | 21 | 279 | 10 | 1 | 10.0000 | |
| dgrover-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 97.7049 | 96.8468 | 98.5782 | 88.2123 | 645 | 21 | 624 | 9 | 3 | 33.3333 | |
| dgrover-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 97.7049 | 96.8468 | 98.5782 | 88.2123 | 645 | 21 | 624 | 9 | 3 | 33.3333 | |
| dgrover-gatk | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 95.7511 | 92.4731 | 99.2701 | 67.4197 | 258 | 21 | 272 | 2 | 2 | 100.0000 | |
| dgrover-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 98.7710 | 98.6981 | 98.8439 | 73.8011 | 1592 | 21 | 1539 | 18 | 13 | 72.2222 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.0176 | 98.6372 | 99.4008 | 77.5553 | 1520 | 21 | 1493 | 9 | 3 | 33.3333 | |
| dgrover-gatk | SNP | tv | HG002compoundhet | * | 99.7478 | 99.7647 | 99.7310 | 49.0520 | 8902 | 21 | 8897 | 24 | 15 | 62.5000 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.5630 | 99.4272 | 99.6991 | 49.6904 | 3645 | 21 | 3645 | 11 | 11 | 100.0000 | |
| rpoplin-dv42 | INDEL | D1_5 | map_l100_m1_e0 | het | 98.4276 | 98.2630 | 98.5927 | 82.4444 | 1188 | 21 | 1191 | 17 | 4 | 23.5294 | |
| rpoplin-dv42 | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 86.0260 | 77.8947 | 96.0526 | 86.8056 | 74 | 21 | 73 | 3 | 1 | 33.3333 | |
| rpoplin-dv42 | INDEL | I1_5 | map_l100_m2_e1 | het | 98.1972 | 97.4074 | 99.0000 | 84.3750 | 789 | 21 | 792 | 8 | 5 | 62.5000 | |
| rpoplin-dv42 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 95.4200 | 94.0678 | 96.8116 | 67.6966 | 333 | 21 | 334 | 11 | 10 | 90.9091 | |
| raldana-dualsentieon | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 96.7812 | 94.0000 | 99.7319 | 34.9040 | 329 | 21 | 372 | 1 | 1 | 100.0000 | |
| raldana-dualsentieon | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.4728 | 99.0810 | 99.8678 | 43.7004 | 2264 | 21 | 2267 | 3 | 0 | 0.0000 | |
| raldana-dualsentieon | INDEL | D1_5 | map_l150_m2_e1 | * | 97.8058 | 97.3008 | 98.3161 | 87.6421 | 757 | 21 | 759 | 13 | 4 | 30.7692 | |
| raldana-dualsentieon | INDEL | I1_5 | map_l100_m1_e0 | het | 97.8051 | 97.2973 | 98.3182 | 81.2333 | 756 | 21 | 760 | 13 | 0 | 0.0000 | |
| raldana-dualsentieon | INDEL | I1_5 | map_l100_m2_e0 | het | 97.8495 | 97.3518 | 98.3523 | 82.6097 | 772 | 21 | 776 | 13 | 0 | 0.0000 | |
| raldana-dualsentieon | INDEL | I1_5 | map_l100_m2_e1 | het | 97.8948 | 97.4074 | 98.3871 | 82.7741 | 789 | 21 | 793 | 13 | 0 | 0.0000 | |
| raldana-dualsentieon | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.6255 | 99.4585 | 99.7930 | 57.9022 | 3857 | 21 | 3857 | 8 | 0 | 0.0000 | |
| raldana-dualsentieon | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.4171 | 99.1580 | 99.6775 | 58.2394 | 2473 | 21 | 2473 | 8 | 0 | 0.0000 | |
| raldana-dualsentieon | SNP | * | map_l250_m1_e0 | homalt | 99.4502 | 99.1474 | 99.7549 | 84.1101 | 2442 | 21 | 2442 | 6 | 3 | 50.0000 | |
| rpoplin-dv42 | INDEL | D16_PLUS | HG002compoundhet | het | 71.2910 | 94.8148 | 57.1195 | 50.0000 | 384 | 21 | 349 | 262 | 262 | 100.0000 | |
| rpoplin-dv42 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 95.7784 | 94.5312 | 97.0588 | 82.6611 | 363 | 21 | 363 | 11 | 5 | 45.4545 | |
| rpoplin-dv42 | INDEL | D16_PLUS | map_l100_m2_e1 | * | 84.4444 | 78.3505 | 91.5663 | 89.1503 | 76 | 21 | 76 | 7 | 3 | 42.8571 | |
| hfeng-pmm2 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.4917 | 99.0340 | 99.9536 | 62.8172 | 2153 | 21 | 2153 | 1 | 0 | 0.0000 | |
| hfeng-pmm2 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.2012 | 98.4859 | 99.9268 | 62.0594 | 1366 | 21 | 1366 | 1 | 0 | 0.0000 | |
| jlack-gatk | INDEL | * | map_siren | hetalt | 95.3604 | 91.4980 | 99.5633 | 86.9812 | 226 | 21 | 228 | 1 | 0 | 0.0000 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 88.8783 | 96.8421 | 82.1248 | 85.9711 | 644 | 21 | 487 | 106 | 95 | 89.6226 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 96.5816 | 99.2511 | 94.0520 | 47.6931 | 2783 | 21 | 2783 | 176 | 175 | 99.4318 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 96.9473 | 99.3365 | 94.6703 | 50.0000 | 3144 | 21 | 3144 | 177 | 175 | 98.8701 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 94.9153 | 90.3226 | 100.0000 | 39.1176 | 196 | 21 | 207 | 0 | 0 | ||
| jlack-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.8835 | 99.1132 | 98.6549 | 87.3860 | 2347 | 21 | 2347 | 32 | 17 | 53.1250 | |
| jlack-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 99.1302 | 99.5045 | 98.7588 | 79.7621 | 4217 | 21 | 4217 | 53 | 8 | 15.0943 | |
| jli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 95.0712 | 90.9871 | 99.5392 | 72.7044 | 212 | 21 | 216 | 1 | 1 | 100.0000 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 99.0629 | 98.1432 | 100.0000 | 42.5707 | 1110 | 21 | 1117 | 0 | 0 | ||
| hfeng-pmm1 | INDEL | I1_5 | map_l100_m1_e0 | het | 98.3748 | 97.2973 | 99.4764 | 82.8507 | 756 | 21 | 760 | 4 | 0 | 0.0000 | |
| hfeng-pmm1 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 97.5435 | 96.5174 | 98.5915 | 71.2841 | 582 | 21 | 560 | 8 | 4 | 50.0000 | |
| hfeng-pmm1 | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 97.1619 | 95.6967 | 98.6726 | 81.7078 | 467 | 21 | 446 | 6 | 1 | 16.6667 | |
| hfeng-pmm1 | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 98.3347 | 96.7239 | 100.0000 | 43.9244 | 620 | 21 | 623 | 0 | 0 | ||
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.4129 | 99.0178 | 99.8112 | 75.1670 | 2117 | 21 | 2115 | 4 | 1 | 25.0000 | |
| hfeng-pmm3 | INDEL | D1_5 | map_l100_m2_e0 | * | 99.0853 | 98.9034 | 99.2678 | 81.4098 | 1894 | 21 | 1898 | 14 | 3 | 21.4286 | |
| hfeng-pmm3 | INDEL | D1_5 | map_l100_m2_e1 | * | 99.0966 | 98.9170 | 99.2769 | 81.5232 | 1918 | 21 | 1922 | 14 | 3 | 21.4286 | |