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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
69201-69250 / 86044 show all | |||||||||||||||
| ckim-gatk | INDEL | D1_5 | segdup | het | 97.3199 | 99.5665 | 95.1724 | 96.5122 | 689 | 3 | 690 | 35 | 0 | 0.0000 | |
| cchapple-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 97.7466 | 96.0553 | 99.4986 | 53.1009 | 2362 | 97 | 6945 | 35 | 29 | 82.8571 | |
| cchapple-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.0840 | 95.2463 | 98.9940 | 50.7712 | 3326 | 166 | 3444 | 35 | 32 | 91.4286 | |
| cchapple-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.6597 | 99.8868 | 99.4337 | 56.4666 | 6177 | 7 | 6145 | 35 | 2 | 5.7143 | |
| cchapple-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.5174 | 99.9237 | 99.1144 | 60.1090 | 3928 | 3 | 3917 | 35 | 2 | 5.7143 | |
| cchapple-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 97.0578 | 96.0317 | 98.1061 | 87.2243 | 1694 | 70 | 1813 | 35 | 22 | 62.8571 | |
| cchapple-custom | SNP | ti | map_l250_m0_e0 | * | 95.9625 | 94.5985 | 97.3664 | 93.5930 | 1296 | 74 | 1294 | 35 | 13 | 37.1429 | |
| cchapple-custom | SNP | tv | func_cds | * | 99.5556 | 99.9085 | 99.2053 | 32.6708 | 4367 | 4 | 4369 | 35 | 0 | 0.0000 | |
| cchapple-custom | SNP | tv | func_cds | het | 99.2733 | 99.8495 | 98.7037 | 37.1216 | 2653 | 4 | 2665 | 35 | 0 | 0.0000 | |
| ckim-isaac | INDEL | * | map_l100_m2_e0 | het | 84.2881 | 73.9489 | 97.9885 | 86.2255 | 1706 | 601 | 1705 | 35 | 15 | 42.8571 | |
| ckim-dragen | INDEL | I1_5 | HG002compoundhet | het | 97.0139 | 98.3529 | 95.7108 | 85.3685 | 836 | 14 | 781 | 35 | 32 | 91.4286 | |
| ckim-dragen | SNP | * | map_l100_m1_e0 | homalt | 99.6437 | 99.4186 | 99.8698 | 55.6951 | 26846 | 157 | 26851 | 35 | 32 | 91.4286 | |
| gduggal-snapfb | INDEL | D1_5 | map_l150_m1_e0 | het | 94.3674 | 95.8506 | 92.9293 | 85.6812 | 462 | 20 | 460 | 35 | 5 | 14.2857 | |
| gduggal-snapfb | INDEL | D1_5 | map_l150_m2_e0 | het | 94.7138 | 96.1089 | 93.3586 | 86.7121 | 494 | 20 | 492 | 35 | 5 | 14.2857 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 54.3642 | 39.0110 | 89.6450 | 28.3898 | 923 | 1443 | 303 | 35 | 34 | 97.1429 | |
| ghariani-varprowl | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 79.1991 | 87.0370 | 72.6562 | 76.5138 | 94 | 14 | 93 | 35 | 35 | 100.0000 | |
| ghariani-varprowl | SNP | ti | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.1675 | 99.9091 | 98.4368 | 44.5929 | 2199 | 2 | 2204 | 35 | 13 | 37.1429 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_51to200 | homalt | 55.8376 | 84.6154 | 41.6667 | 48.2759 | 11 | 2 | 25 | 35 | 28 | 80.0000 | |
| gduggal-snapplat | INDEL | I1_5 | segdup | homalt | 83.8070 | 77.3784 | 91.4005 | 94.4573 | 366 | 107 | 372 | 35 | 2 | 5.7143 | |
| gduggal-snapplat | INDEL | * | map_l250_m2_e0 | het | 74.7095 | 69.0476 | 81.3830 | 98.2825 | 145 | 65 | 153 | 35 | 5 | 14.2857 | |
| gduggal-snapplat | INDEL | * | map_l250_m2_e1 | het | 74.8369 | 69.1943 | 81.4815 | 98.3230 | 146 | 65 | 154 | 35 | 5 | 14.2857 | |
| gduggal-snapvard | INDEL | I6_15 | map_l150_m1_e0 | * | 60.8583 | 72.0000 | 52.7027 | 87.7888 | 18 | 7 | 39 | 35 | 27 | 77.1429 | |
| gduggal-snapvard | INDEL | I6_15 | map_l150_m1_e0 | het | 63.8563 | 93.3333 | 48.5294 | 87.8571 | 14 | 1 | 33 | 35 | 27 | 77.1429 | |
| gduggal-snapvard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 88.9064 | 83.4507 | 95.1253 | 86.7650 | 711 | 141 | 683 | 35 | 18 | 51.4286 | |
| gduggal-snapvard | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 98.3473 | 97.2572 | 99.4621 | 37.7380 | 6560 | 185 | 6472 | 35 | 18 | 51.4286 | |
| gduggal-snapvard | SNP | * | map_l125_m1_e0 | homalt | 97.9102 | 96.1077 | 99.7817 | 66.1808 | 16247 | 658 | 15999 | 35 | 27 | 77.1429 | |
| gduggal-snapvard | SNP | tv | func_cds | * | 98.8510 | 98.5129 | 99.1913 | 36.1464 | 4306 | 65 | 4293 | 35 | 10 | 28.5714 | |
| gduggal-snapplat | SNP | * | map_siren | homalt | 97.4154 | 95.0214 | 99.9332 | 54.3867 | 52410 | 2746 | 52361 | 35 | 23 | 65.7143 | |
| gduggal-snapvard | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 32.8464 | 22.5806 | 60.2273 | 99.9609 | 28 | 96 | 53 | 35 | 24 | 68.5714 | |
| gduggal-snapvard | INDEL | C6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 0.0000 | 0.0000 | 23.9130 | 83.8596 | 0 | 0 | 11 | 35 | 7 | 20.0000 | |
| gduggal-snapvard | SNP | tv | lowcmp_SimpleRepeat_diTR_51to200 | * | 37.3333 | 53.8462 | 28.5714 | 97.4833 | 14 | 12 | 14 | 35 | 1 | 2.8571 | |
| gduggal-snapvard | SNP | tv | lowcmp_SimpleRepeat_diTR_51to200 | het | 26.6667 | 47.0588 | 18.6047 | 97.2132 | 8 | 9 | 8 | 35 | 1 | 2.8571 | |
| ghariani-varprowl | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 49.6593 | 34.5745 | 88.0952 | 72.2117 | 260 | 492 | 259 | 35 | 21 | 60.0000 | |
| hfeng-pmm1 | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.4409 | 98.9502 | 99.9364 | 58.3709 | 55047 | 584 | 55037 | 35 | 12 | 34.2857 | |
| hfeng-pmm1 | SNP | * | map_l100_m1_e0 | homalt | 99.8556 | 99.8408 | 99.8703 | 60.9594 | 26960 | 43 | 26960 | 35 | 17 | 48.5714 | |
| hfeng-pmm1 | SNP | * | map_l100_m2_e0 | homalt | 99.8583 | 99.8438 | 99.8728 | 63.3749 | 27480 | 43 | 27480 | 35 | 17 | 48.5714 | |
| hfeng-pmm1 | SNP | * | map_l100_m2_e1 | homalt | 99.8597 | 99.8453 | 99.8740 | 63.3660 | 27753 | 43 | 27753 | 35 | 17 | 48.5714 | |
| hfeng-pmm1 | SNP | ti | map_l250_m1_e0 | het | 98.6671 | 98.5175 | 98.8172 | 88.8014 | 2924 | 44 | 2924 | 35 | 8 | 22.8571 | |
| hfeng-pmm1 | SNP | ti | map_l250_m2_e0 | het | 98.7844 | 98.6478 | 98.9214 | 88.9993 | 3210 | 44 | 3210 | 35 | 8 | 22.8571 | |
| hfeng-pmm1 | SNP | ti | map_l250_m2_e1 | het | 98.7703 | 98.6056 | 98.9355 | 89.0938 | 3253 | 46 | 3253 | 35 | 8 | 22.8571 | |
| jlack-gatk | SNP | ti | HG002complexvar | homalt | 99.9491 | 99.9163 | 99.9819 | 18.2375 | 193301 | 162 | 193290 | 35 | 32 | 91.4286 | |
| hfeng-pmm2 | SNP | tv | segdup | het | 99.5467 | 99.7541 | 99.3402 | 91.9297 | 5274 | 13 | 5270 | 35 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.0292 | 97.0795 | 98.9977 | 67.6517 | 3457 | 104 | 3457 | 35 | 30 | 85.7143 | |
| hfeng-pmm2 | INDEL | I6_15 | HG002complexvar | homalt | 98.4965 | 99.8353 | 97.1933 | 55.2244 | 1212 | 2 | 1212 | 35 | 35 | 100.0000 | |
| hfeng-pmm2 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 96.6488 | 94.3546 | 99.0574 | 55.6339 | 3677 | 220 | 3678 | 35 | 28 | 80.0000 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 96.9617 | 96.7357 | 97.1888 | 78.6888 | 1215 | 41 | 1210 | 35 | 17 | 48.5714 | |
| jlack-gatk | INDEL | D6_15 | HG002compoundhet | hetalt | 94.7748 | 90.4552 | 99.5278 | 24.3596 | 7373 | 778 | 7377 | 35 | 30 | 85.7143 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.6991 | 97.6504 | 99.7706 | 72.0664 | 15211 | 366 | 15219 | 35 | 25 | 71.4286 | |
| hfeng-pmm3 | SNP | * | map_l100_m1_e0 | homalt | 99.8518 | 99.8334 | 99.8703 | 60.8633 | 26958 | 45 | 26958 | 35 | 17 | 48.5714 | |
| hfeng-pmm3 | SNP | * | map_l100_m2_e0 | homalt | 99.8546 | 99.8365 | 99.8728 | 63.2901 | 27478 | 45 | 27478 | 35 | 17 | 48.5714 | |