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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
65651-65700 / 86044 show all | |||||||||||||||
| hfeng-pmm2 | INDEL | D1_5 | map_l125_m0_e0 | * | 97.6181 | 98.9919 | 96.2818 | 88.4650 | 491 | 5 | 492 | 19 | 3 | 15.7895 | |
| hfeng-pmm2 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 94.9772 | 98.5782 | 91.6300 | 69.1156 | 208 | 3 | 208 | 19 | 18 | 94.7368 | |
| hfeng-pmm3 | SNP | tv | map_l250_m1_e0 | het | 98.3966 | 97.8735 | 98.9253 | 88.0822 | 1749 | 38 | 1749 | 19 | 0 | 0.0000 | |
| jlack-gatk | INDEL | * | func_cds | het | 95.7871 | 100.0000 | 91.9149 | 63.3385 | 214 | 0 | 216 | 19 | 0 | 0.0000 | |
| jlack-gatk | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 89.0056 | 80.5701 | 99.4139 | 40.3057 | 3081 | 743 | 3223 | 19 | 17 | 89.4737 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.3938 | 98.5294 | 98.2585 | 65.1438 | 1072 | 16 | 1072 | 19 | 14 | 73.6842 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 97.3321 | 96.2662 | 98.4219 | 60.3556 | 1186 | 46 | 1185 | 19 | 18 | 94.7368 | |
| jlack-gatk | INDEL | D6_15 | segdup | * | 92.8571 | 95.2880 | 90.5473 | 94.7561 | 182 | 9 | 182 | 19 | 5 | 26.3158 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.5017 | 97.5265 | 93.5593 | 68.9474 | 276 | 7 | 276 | 19 | 19 | 100.0000 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.8242 | 99.0991 | 98.5507 | 72.0171 | 1320 | 12 | 1292 | 19 | 15 | 78.9474 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 86.1314 | 100.0000 | 75.6410 | 73.7374 | 59 | 0 | 59 | 19 | 19 | 100.0000 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 94.1538 | 100.0000 | 88.9535 | 77.1580 | 153 | 0 | 153 | 19 | 18 | 94.7368 | |
| jlack-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 98.6014 | 99.4125 | 97.8035 | 88.8214 | 846 | 5 | 846 | 19 | 8 | 42.1053 | |
| jlack-gatk | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | het | 99.4922 | 99.5870 | 99.3976 | 71.7079 | 3135 | 13 | 3135 | 19 | 9 | 47.3684 | |
| jlack-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.6982 | 98.8933 | 98.5039 | 87.7567 | 1251 | 14 | 1251 | 19 | 13 | 68.4211 | |
| jli-custom | INDEL | * | map_siren | homalt | 99.3607 | 99.4350 | 99.2865 | 79.8135 | 2640 | 15 | 2644 | 19 | 11 | 57.8947 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.5480 | 99.6325 | 99.4637 | 71.3697 | 3524 | 13 | 3524 | 19 | 19 | 100.0000 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 96.9781 | 94.7333 | 99.3319 | 50.0000 | 2824 | 157 | 2825 | 19 | 16 | 84.2105 | |
| hfeng-pmm3 | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.4357 | 98.9449 | 99.9314 | 53.1567 | 27664 | 295 | 27664 | 19 | 7 | 36.8421 | |
| hfeng-pmm1 | INDEL | * | segdup | het | 98.8075 | 98.9086 | 98.7066 | 94.4130 | 1450 | 16 | 1450 | 19 | 0 | 0.0000 | |
| hfeng-pmm1 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.2475 | 95.8170 | 98.7214 | 83.8109 | 1466 | 64 | 1467 | 19 | 9 | 47.3684 | |
| hfeng-pmm1 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.2475 | 95.8170 | 98.7214 | 83.8109 | 1466 | 64 | 1467 | 19 | 9 | 47.3684 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 97.9808 | 97.2102 | 98.7638 | 71.4047 | 1568 | 45 | 1518 | 19 | 12 | 63.1579 | |
| hfeng-pmm1 | INDEL | * | map_l150_m2_e1 | * | 97.5801 | 96.5949 | 98.5856 | 88.8230 | 1390 | 49 | 1394 | 20 | 4 | 20.0000 | |
| hfeng-pmm1 | INDEL | D6_15 | HG002complexvar | het | 95.9519 | 92.8205 | 99.3019 | 57.0271 | 2896 | 224 | 2845 | 20 | 17 | 85.0000 | |
| hfeng-pmm1 | INDEL | I1_5 | HG002complexvar | homalt | 99.8625 | 99.8736 | 99.8514 | 52.0252 | 13431 | 17 | 13435 | 20 | 17 | 85.0000 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.5198 | 99.6042 | 99.4355 | 71.4918 | 3523 | 14 | 3523 | 20 | 20 | 100.0000 | |
| 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-pmm2 | INDEL | D6_15 | HG002complexvar | het | 95.8142 | 92.5641 | 99.3009 | 57.1386 | 2888 | 232 | 2841 | 20 | 16 | 80.0000 | |
| hfeng-pmm2 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 96.9762 | 95.3595 | 98.6486 | 84.3187 | 1459 | 71 | 1460 | 20 | 10 | 50.0000 | |
| hfeng-pmm2 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 96.9762 | 95.3595 | 98.6486 | 84.3187 | 1459 | 71 | 1460 | 20 | 10 | 50.0000 | |
| hfeng-pmm2 | SNP | * | HG002compoundhet | het | 95.9129 | 92.2768 | 99.8474 | 42.7742 | 13083 | 1095 | 13083 | 20 | 3 | 15.0000 | |
| hfeng-pmm2 | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 97.6573 | 96.0544 | 99.3146 | 65.3032 | 2897 | 119 | 2898 | 20 | 0 | 0.0000 | |
| hfeng-pmm2 | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.0510 | 98.2298 | 99.8861 | 53.8211 | 17535 | 316 | 17534 | 20 | 1 | 5.0000 | |
| hfeng-pmm2 | SNP | tv | map_l250_m0_e0 | het | 97.0435 | 97.5524 | 96.5398 | 93.4041 | 558 | 14 | 558 | 20 | 1 | 5.0000 | |
| hfeng-pmm3 | INDEL | * | map_l100_m0_e0 | het | 98.1428 | 98.2370 | 98.0488 | 85.0974 | 1003 | 18 | 1005 | 20 | 2 | 10.0000 | |
| hfeng-pmm3 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.6271 | 96.4286 | 98.8558 | 65.7524 | 1728 | 64 | 1728 | 20 | 18 | 90.0000 | |
| hfeng-pmm3 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | het | 95.0004 | 93.9245 | 96.1014 | 81.4130 | 572 | 37 | 493 | 20 | 18 | 90.0000 | |
| hfeng-pmm1 | SNP | ti | map_l250_m0_e0 | het | 97.9133 | 97.9657 | 97.8610 | 93.2569 | 915 | 19 | 915 | 20 | 3 | 15.0000 | |
| hfeng-pmm1 | SNP | tv | map_l250_m1_e0 | het | 98.1685 | 97.4818 | 98.8649 | 87.9315 | 1742 | 45 | 1742 | 20 | 2 | 10.0000 | |
| hfeng-pmm2 | INDEL | * | map_l150_m0_e0 | * | 97.3151 | 98.4436 | 96.2121 | 92.3077 | 506 | 8 | 508 | 20 | 4 | 20.0000 | |
| hfeng-pmm2 | INDEL | * | segdup | * | 99.0994 | 98.9828 | 99.2163 | 94.4475 | 2530 | 26 | 2532 | 20 | 4 | 20.0000 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | * | 78.5775 | 66.5710 | 95.8678 | 49.7925 | 464 | 233 | 464 | 20 | 18 | 90.0000 | |
| hfeng-pmm3 | INDEL | D1_5 | map_siren | * | 99.3769 | 99.3199 | 99.4339 | 78.1455 | 3505 | 24 | 3513 | 20 | 5 | 25.0000 | |
| jlack-gatk | INDEL | * | func_cds | * | 97.6994 | 99.7753 | 95.7082 | 54.1790 | 444 | 1 | 446 | 20 | 1 | 5.0000 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.5173 | 99.5860 | 99.4487 | 75.8037 | 3608 | 15 | 3608 | 20 | 9 | 45.0000 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | * | 96.2345 | 95.7792 | 96.6942 | 67.4731 | 590 | 26 | 585 | 20 | 16 | 80.0000 | |
| jlack-gatk | INDEL | D16_PLUS | map_siren | * | 89.0690 | 91.6084 | 86.6667 | 94.5750 | 131 | 12 | 130 | 20 | 3 | 15.0000 | |
| jlack-gatk | INDEL | D6_15 | HG002complexvar | homalt | 99.0234 | 99.7434 | 98.3137 | 61.3807 | 1166 | 3 | 1166 | 20 | 19 | 95.0000 | |
| jlack-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 98.6913 | 98.9198 | 98.4639 | 87.5787 | 1282 | 14 | 1282 | 20 | 9 | 45.0000 | |