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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
60151-60200 / 86044 show all | |||||||||||||||
| dgrover-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.0855 | 99.3885 | 98.7844 | 71.5296 | 3738 | 23 | 3738 | 46 | 44 | 95.6522 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.3958 | 98.0100 | 98.7847 | 73.2093 | 591 | 12 | 569 | 7 | 3 | 42.8571 | |
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.3958 | 98.0100 | 98.7847 | 72.5975 | 591 | 12 | 569 | 7 | 3 | 42.8571 | |
| hfeng-pmm1 | INDEL | D1_5 | map_l100_m0_e0 | het | 97.4281 | 96.1083 | 98.7847 | 80.3413 | 568 | 23 | 569 | 7 | 0 | 0.0000 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 95.2032 | 91.8723 | 98.7848 | 43.0326 | 2532 | 224 | 2520 | 31 | 30 | 96.7742 | |
| egarrison-hhga | INDEL | I1_5 | map_l125_m2_e0 | het | 98.4864 | 98.1891 | 98.7854 | 87.7084 | 488 | 9 | 488 | 6 | 1 | 16.6667 | |
| gduggal-bwafb | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 97.5025 | 96.2525 | 98.7854 | 87.2812 | 488 | 19 | 488 | 6 | 5 | 83.3333 | |
| astatham-gatk | INDEL | * | map_l150_m2_e1 | homalt | 98.9858 | 99.1870 | 98.7854 | 89.4512 | 488 | 4 | 488 | 6 | 4 | 66.6667 | |
| hfeng-pmm2 | INDEL | * | map_l150_m2_e1 | homalt | 98.9858 | 99.1870 | 98.7854 | 88.2938 | 488 | 4 | 488 | 6 | 4 | 66.6667 | |
| gduggal-bwafb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 94.6807 | 90.9033 | 98.7857 | 42.8578 | 11382 | 1139 | 23592 | 290 | 233 | 80.3448 | |
| mlin-fermikit | SNP | ti | map_l150_m0_e0 | het | 44.5289 | 28.7424 | 98.7862 | 66.7936 | 1465 | 3632 | 1465 | 18 | 3 | 16.6667 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.0207 | 95.3171 | 98.7864 | 34.4210 | 6493 | 319 | 6512 | 80 | 77 | 96.2500 | |
| gduggal-bwaplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 84.3152 | 73.5419 | 98.7866 | 76.1775 | 1387 | 499 | 1384 | 17 | 13 | 76.4706 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 97.1229 | 95.5140 | 98.7868 | 83.6312 | 511 | 24 | 570 | 7 | 7 | 100.0000 | |
| jmaeng-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 96.3724 | 94.0724 | 98.7877 | 56.0658 | 3666 | 231 | 3667 | 45 | 39 | 86.6667 | |
| ltrigg-rtg1 | INDEL | * | map_l150_m0_e0 | homalt | 99.0881 | 99.3902 | 98.7879 | 89.8148 | 163 | 1 | 163 | 2 | 2 | 100.0000 | |
| jpowers-varprowl | INDEL | D1_5 | map_l125_m1_e0 | homalt | 96.0236 | 93.4097 | 98.7879 | 81.0454 | 326 | 23 | 326 | 4 | 1 | 25.0000 | |
| ckim-vqsr | INDEL | * | map_l150_m0_e0 | homalt | 99.0881 | 99.3902 | 98.7879 | 91.7376 | 163 | 1 | 163 | 2 | 2 | 100.0000 | |
| dgrover-gatk | INDEL | I1_5 | map_l125_m2_e0 | het | 98.3863 | 97.9879 | 98.7879 | 88.9681 | 487 | 10 | 489 | 6 | 0 | 0.0000 | |
| ckim-dragen | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 95.0437 | 91.5730 | 98.7879 | 71.6007 | 163 | 15 | 163 | 2 | 1 | 50.0000 | |
| gduggal-bwaplat | INDEL | D1_5 | map_l100_m2_e1 | * | 82.9443 | 71.4801 | 98.7883 | 92.1357 | 1386 | 553 | 1386 | 17 | 7 | 41.1765 | |
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 96.9900 | 95.2557 | 98.7886 | 47.4309 | 13131 | 654 | 13129 | 161 | 155 | 96.2733 | |
| hfeng-pmm2 | SNP | tv | map_l125_m2_e0 | het | 99.0157 | 99.2434 | 98.7891 | 75.7772 | 10363 | 79 | 10361 | 127 | 11 | 8.6614 | |
| ndellapenna-hhga | INDEL | D1_5 | * | hetalt | 77.7578 | 64.1093 | 98.7893 | 70.8854 | 6568 | 3677 | 6120 | 75 | 63 | 84.0000 | |
| asubramanian-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 98.0755 | 97.3713 | 98.7899 | 89.5852 | 889 | 24 | 898 | 11 | 9 | 81.8182 | |
| jli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 99.3497 | 99.9156 | 98.7902 | 51.5758 | 2368 | 2 | 2368 | 29 | 29 | 100.0000 | |
| jli-custom | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.9276 | 97.0798 | 98.7903 | 74.9326 | 1496 | 45 | 1470 | 18 | 5 | 27.7778 | |
| ndellapenna-hhga | INDEL | D1_5 | map_l150_m2_e1 | homalt | 98.7903 | 98.7903 | 98.7903 | 87.8491 | 245 | 3 | 245 | 3 | 3 | 100.0000 | |
| raldana-dualsentieon | INDEL | D6_15 | map_siren | * | 97.5124 | 96.2672 | 98.7903 | 81.9898 | 490 | 19 | 490 | 6 | 2 | 33.3333 | |
| rpoplin-dv42 | SNP | ti | map_l250_m1_e0 | * | 98.4440 | 98.1000 | 98.7904 | 87.6879 | 4492 | 87 | 4492 | 55 | 36 | 65.4545 | |
| dgrover-gatk | SNP | tv | map_l125_m2_e0 | het | 99.0688 | 99.3488 | 98.7904 | 77.6779 | 10374 | 68 | 10372 | 127 | 22 | 17.3228 | |
| jpowers-varprowl | SNP | * | map_siren | * | 98.5825 | 98.3751 | 98.7907 | 60.8110 | 143852 | 2376 | 143855 | 1761 | 441 | 25.0426 | |
| hfeng-pmm1 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 91.2134 | 84.7150 | 98.7915 | 90.8715 | 327 | 59 | 327 | 4 | 0 | 0.0000 | |
| gduggal-bwaplat | INDEL | D1_5 | map_l100_m1_e0 | * | 82.4716 | 70.7792 | 98.7915 | 91.7846 | 1308 | 540 | 1308 | 16 | 6 | 37.5000 | |
| ndellapenna-hhga | INDEL | * | map_siren | homalt | 98.6802 | 98.5687 | 98.7920 | 79.0989 | 2617 | 38 | 2617 | 32 | 23 | 71.8750 | |
| gduggal-bwafb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 91.1195 | 84.5528 | 98.7921 | 74.4432 | 1144 | 209 | 1145 | 14 | 13 | 92.8571 | |
| bgallagher-sentieon | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.3464 | 99.9061 | 98.7929 | 68.3700 | 1064 | 1 | 1064 | 13 | 13 | 100.0000 | |
| gduggal-bwafb | SNP | ti | map_siren | het | 99.0568 | 99.3219 | 98.7930 | 59.4400 | 61959 | 423 | 61963 | 757 | 131 | 17.3052 | |
| rpoplin-dv42 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.0325 | 97.2835 | 98.7931 | 73.7259 | 1146 | 32 | 1146 | 14 | 13 | 92.8571 | |
| egarrison-hhga | INDEL | I1_5 | map_l125_m1_e0 | * | 98.7342 | 98.6747 | 98.7937 | 86.0391 | 819 | 11 | 819 | 10 | 2 | 20.0000 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 98.7939 | 98.7939 | 98.7939 | 70.6564 | 901 | 11 | 901 | 11 | 9 | 81.8182 | |
| jli-custom | INDEL | * | map_l100_m2_e1 | * | 98.4239 | 98.0564 | 98.7942 | 84.0281 | 3683 | 73 | 3687 | 45 | 15 | 33.3333 | |
| gduggal-bwaplat | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 88.2228 | 79.6951 | 98.7942 | 76.5609 | 24515 | 6246 | 24497 | 299 | 252 | 84.2809 | |
| jli-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 99.2014 | 99.6118 | 98.7944 | 67.9415 | 19503 | 76 | 19503 | 238 | 15 | 6.3025 | |
| jli-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 99.2014 | 99.6118 | 98.7944 | 67.9415 | 19503 | 76 | 19503 | 238 | 15 | 6.3025 | |
| jlack-gatk | SNP | tv | * | het | 99.3606 | 99.9332 | 98.7945 | 31.3268 | 591301 | 395 | 591230 | 7214 | 153 | 2.1209 | |
| ckim-isaac | INDEL | D1_5 | * | * | 97.5429 | 96.3222 | 98.7949 | 47.4402 | 141348 | 5397 | 141168 | 1722 | 1190 | 69.1057 | |
| egarrison-hhga | INDEL | D1_5 | map_l150_m0_e0 | homalt | 97.6190 | 96.4706 | 98.7952 | 90.8691 | 82 | 3 | 82 | 1 | 1 | 100.0000 | |
| dgrover-gatk | INDEL | D6_15 | map_l150_m2_e1 | * | 97.6190 | 96.4706 | 98.7952 | 93.1120 | 82 | 3 | 82 | 1 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.8024 | 98.8095 | 98.7952 | 79.2500 | 166 | 2 | 164 | 2 | 1 | 50.0000 | |