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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
2651-2700 / 86044 show all | |||||||||||||||
| eyeh-varpipe | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 58.5321 | 47.8735 | 75.2959 | 43.8204 | 2544 | 2770 | 8714 | 2859 | 2841 | 99.3704 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 87.7988 | 86.5556 | 89.0781 | 44.8149 | 17827 | 2769 | 18620 | 2283 | 1417 | 62.0675 | |
| gduggal-snapplat | SNP | ti | map_l100_m2_e1 | * | 95.8022 | 94.4145 | 97.2313 | 76.1409 | 46721 | 2764 | 46742 | 1331 | 691 | 51.9159 | |
| ckim-gatk | SNP | tv | map_l100_m2_e1 | homalt | 82.5549 | 70.3075 | 99.9694 | 70.5594 | 6540 | 2762 | 6540 | 2 | 0 | 0.0000 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 87.6898 | 82.8388 | 93.1443 | 61.7926 | 13318 | 2759 | 13301 | 979 | 950 | 97.0378 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 87.6898 | 82.8388 | 93.1443 | 61.7926 | 13318 | 2759 | 13301 | 979 | 950 | 97.0378 | |
| gduggal-snapfb | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 80.6675 | 73.6706 | 89.1329 | 45.4946 | 7717 | 2758 | 2313 | 282 | 188 | 66.6667 | |
| gduggal-snapplat | SNP | ti | map_l100_m2_e0 | * | 95.7724 | 94.3751 | 97.2116 | 76.1299 | 46207 | 2754 | 46228 | 1326 | 687 | 51.8100 | |
| ghariani-varprowl | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 47.8508 | 44.9290 | 51.1791 | 74.3426 | 2246 | 2753 | 2257 | 2153 | 2109 | 97.9563 | |
| ghariani-varprowl | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 47.8508 | 44.9290 | 51.1791 | 74.3426 | 2246 | 2753 | 2257 | 2153 | 2109 | 97.9563 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 77.1982 | 70.9029 | 84.7203 | 46.8070 | 6706 | 2752 | 6831 | 1232 | 1026 | 83.2792 | |
| ckim-gatk | SNP | tv | map_l100_m2_e0 | homalt | 82.4340 | 70.1324 | 99.9691 | 70.6315 | 6462 | 2752 | 6462 | 2 | 0 | 0.0000 | |
| gduggal-bwaplat | SNP | * | map_l150_m0_e0 | homalt | 49.2722 | 32.6975 | 99.9253 | 90.1218 | 1337 | 2752 | 1337 | 1 | 1 | 100.0000 | |
| jmaeng-gatk | SNP | tv | map_l100_m2_e1 | homalt | 82.6342 | 70.4150 | 99.9847 | 69.7916 | 6550 | 2752 | 6550 | 1 | 1 | 100.0000 | |
| gduggal-snapplat | SNP | * | map_siren | homalt | 97.4154 | 95.0214 | 99.9332 | 54.3867 | 52410 | 2746 | 52361 | 35 | 23 | 65.7143 | |
| ckim-gatk | SNP | tv | map_l100_m1_e0 | homalt | 82.0884 | 69.6340 | 99.9682 | 68.5726 | 6297 | 2746 | 6297 | 2 | 0 | 0.0000 | |
| gduggal-snapvard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 86.9733 | 91.1887 | 83.1303 | 79.6742 | 28398 | 2744 | 28182 | 5719 | 224 | 3.9168 | |
| gduggal-snapvard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 86.9733 | 91.1887 | 83.1303 | 79.6742 | 28398 | 2744 | 28182 | 5719 | 224 | 3.9168 | |
| jmaeng-gatk | SNP | tv | map_l100_m2_e0 | homalt | 82.5067 | 70.2301 | 99.9845 | 69.8682 | 6471 | 2743 | 6471 | 1 | 1 | 100.0000 | |
| ltrigg-rtg1 | INDEL | * | * | het | 99.1142 | 98.5886 | 99.6455 | 55.1307 | 191393 | 2740 | 190584 | 678 | 162 | 23.8938 | |
| jmaeng-gatk | SNP | tv | map_l100_m1_e0 | homalt | 82.1629 | 69.7335 | 99.9841 | 67.6746 | 6306 | 2737 | 6306 | 1 | 1 | 100.0000 | |
| gduggal-snapplat | SNP | ti | map_l100_m1_e0 | * | 95.7091 | 94.2918 | 97.1698 | 74.6083 | 45195 | 2736 | 45216 | 1317 | 683 | 51.8603 | |
| qzeng-custom | SNP | tv | map_l100_m0_e0 | * | 84.6327 | 75.3158 | 96.5801 | 84.0828 | 8348 | 2736 | 8331 | 295 | 249 | 84.4068 | |
| gduggal-bwaplat | INDEL | D6_15 | HG002compoundhet | * | 81.3435 | 69.7154 | 97.6272 | 45.9650 | 6296 | 2735 | 6295 | 153 | 109 | 71.2418 | |
| gduggal-snapfb | INDEL | I1_5 | HG002compoundhet | * | 77.3920 | 77.8731 | 76.9169 | 63.1671 | 9622 | 2734 | 10473 | 3143 | 1735 | 55.2020 | |
| ciseli-custom | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 35.0447 | 30.4403 | 41.2903 | 53.1797 | 1196 | 2733 | 1216 | 1729 | 1499 | 86.6975 | |
| gduggal-snapplat | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 90.2475 | 83.3770 | 98.3520 | 63.7948 | 13698 | 2731 | 13726 | 230 | 21 | 9.1304 | |
| anovak-vg | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 0.0000 | 32.2661 | 0.0000 | 0.0000 | 1300 | 2729 | 0 | 0 | 0 | ||
| gduggal-snapplat | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 42.7404 | 30.1771 | 73.2258 | 61.7378 | 1176 | 2721 | 1135 | 415 | 63 | 15.1807 | |
| gduggal-snapplat | INDEL | I16_PLUS | * | het | 0.0000 | 0.0000 | 0.0000 | 0 | 2718 | 0 | 0 | 0 | |||
| gduggal-bwavard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 0.0000 | 0.1836 | 0.0000 | 0.0000 | 5 | 2718 | 0 | 0 | 0 | ||
| gduggal-snapfb | INDEL | I16_PLUS | * | het | 0.0000 | 0.0736 | 0.0000 | 0.0000 | 2 | 2716 | 0 | 0 | 0 | ||
| bgallagher-sentieon | INDEL | * | * | * | 99.2678 | 99.2143 | 99.3213 | 59.6036 | 341835 | 2707 | 341703 | 2335 | 1924 | 82.3983 | |
| jpowers-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 0.0000 | 0.5876 | 0.0000 | 0.0000 | 16 | 2707 | 0 | 0 | 0 | ||
| anovak-vg | SNP | * | map_l125_m1_e0 | het | 77.1793 | 90.4691 | 67.2939 | 76.7918 | 25686 | 2706 | 25425 | 12357 | 2688 | 21.7529 | |
| ghariani-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 0.0000 | 0.6243 | 0.0000 | 0.0000 | 17 | 2706 | 0 | 0 | 0 | ||
| anovak-vg | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 32.2728 | 22.6804 | 55.9262 | 35.3818 | 792 | 2700 | 1576 | 1242 | 1045 | 84.1385 | |
| gduggal-bwaplat | INDEL | I16_PLUS | * | * | 72.4372 | 57.6760 | 97.3531 | 65.4535 | 3678 | 2699 | 3678 | 100 | 83 | 83.0000 | |
| qzeng-custom | SNP | * | map_l250_m1_e0 | * | 74.6091 | 62.6419 | 92.2286 | 95.4856 | 4524 | 2698 | 4486 | 378 | 314 | 83.0688 | |
| qzeng-custom | INDEL | I6_15 | HG002compoundhet | * | 75.9258 | 69.2571 | 84.0157 | 36.6439 | 6078 | 2698 | 5992 | 1140 | 884 | 77.5439 | |
| mlin-fermikit | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 82.9460 | 70.9983 | 99.7285 | 65.0277 | 6600 | 2696 | 6611 | 18 | 18 | 100.0000 | |
| gduggal-bwafb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 93.8883 | 91.5760 | 96.3203 | 46.9726 | 29297 | 2695 | 34055 | 1301 | 1239 | 95.2344 | |
| gduggal-bwafb | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 94.4932 | 92.6377 | 96.4246 | 45.4241 | 33898 | 2694 | 37756 | 1400 | 1310 | 93.5714 | |
| gduggal-bwaplat | INDEL | D1_5 | * | hetalt | 83.8440 | 73.7042 | 97.2186 | 75.9425 | 7551 | 2694 | 7550 | 216 | 214 | 99.0741 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 37.3916 | 32.4297 | 44.1462 | 77.4584 | 1292 | 2692 | 1776 | 2247 | 890 | 39.6084 | |
| jpowers-varprowl | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 39.0386 | 32.6054 | 48.6345 | 60.4703 | 1299 | 2685 | 1300 | 1373 | 1338 | 97.4508 | |
| gduggal-bwaplat | INDEL | D1_5 | HG002compoundhet | hetalt | 84.6945 | 73.7471 | 99.4587 | 70.0372 | 7534 | 2682 | 7533 | 41 | 39 | 95.1220 | |
| jpowers-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 53.6407 | 81.6652 | 39.9361 | 49.3327 | 11937 | 2680 | 12008 | 18060 | 17978 | 99.5460 | |
| ltrigg-rtg1 | SNP | * | * | het | 99.8185 | 99.8570 | 99.7799 | 17.5567 | 1870919 | 2679 | 1871167 | 4127 | 102 | 2.4715 | |
| qzeng-custom | INDEL | I6_15 | * | hetalt | 81.2294 | 68.6820 | 99.3860 | 39.2080 | 5873 | 2678 | 3723 | 23 | 17 | 73.9130 | |