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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
15401-15450 / 86044 show all | |||||||||||||||
| hfeng-pmm3 | SNP | ti | map_l150_m2_e0 | * | 99.5024 | 99.4394 | 99.5655 | 75.5202 | 20397 | 115 | 20393 | 89 | 14 | 15.7303 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.4946 | 98.2087 | 98.7822 | 76.6731 | 6305 | 115 | 6246 | 77 | 38 | 49.3506 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.4946 | 98.2087 | 98.7822 | 76.6731 | 6305 | 115 | 6246 | 77 | 38 | 49.3506 | |
| jlack-gatk | SNP | tv | map_l125_m0_e0 | * | 93.0649 | 98.2657 | 88.3869 | 84.2156 | 6516 | 115 | 6515 | 856 | 54 | 6.3084 | |
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.4714 | 99.0316 | 99.9151 | 48.2190 | 11760 | 115 | 11765 | 10 | 7 | 70.0000 | |
| eyeh-varpipe | SNP | ti | map_l100_m2_e0 | het | 99.0330 | 99.6245 | 98.4486 | 71.1792 | 30507 | 115 | 29825 | 470 | 19 | 4.0426 | |
| eyeh-varpipe | SNP | ti | map_l100_m2_e1 | het | 99.0385 | 99.6286 | 98.4553 | 71.2000 | 30845 | 115 | 30148 | 473 | 19 | 4.0169 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 89.7585 | 88.5572 | 90.9928 | 62.2488 | 890 | 115 | 889 | 88 | 82 | 93.1818 | |
| gduggal-bwafb | SNP | ti | map_l250_m2_e0 | * | 98.0365 | 97.7037 | 98.3715 | 89.9163 | 4893 | 115 | 4893 | 81 | 24 | 29.6296 | |
| gduggal-bwaplat | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 85.6847 | 76.6260 | 97.1722 | 71.5227 | 377 | 115 | 378 | 11 | 10 | 90.9091 | |
| gduggal-bwaplat | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 51.6493 | 35.3933 | 95.5224 | 83.2080 | 63 | 115 | 64 | 3 | 3 | 100.0000 | |
| eyeh-varpipe | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | het | 40.7379 | 29.8780 | 64.0000 | 63.0542 | 49 | 115 | 48 | 27 | 26 | 96.2963 | |
| asubramanian-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 92.1502 | 94.7199 | 89.7161 | 77.6402 | 2063 | 115 | 1928 | 221 | 141 | 63.8009 | |
| bgallagher-sentieon | SNP | tv | HG002complexvar | het | 99.9389 | 99.9237 | 99.9542 | 21.4883 | 150616 | 115 | 150540 | 69 | 21 | 30.4348 | |
| anovak-vg | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | het | 26.2530 | 22.2973 | 31.9149 | 42.5829 | 33 | 115 | 105 | 224 | 205 | 91.5179 | |
| anovak-vg | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 43.2688 | 35.3933 | 55.6522 | 57.2491 | 63 | 115 | 64 | 51 | 38 | 74.5098 | |
| anovak-vg | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 59.9388 | 63.0225 | 57.1429 | 46.3295 | 196 | 115 | 376 | 282 | 235 | 83.3333 | |
| anovak-vg | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | * | 97.3224 | 97.0558 | 97.5904 | 32.2861 | 3791 | 115 | 3807 | 94 | 61 | 64.8936 | |
| ckim-dragen | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.4189 | 94.5959 | 94.2426 | 73.7195 | 2013 | 115 | 1997 | 122 | 101 | 82.7869 | |
| ciseli-custom | INDEL | D1_5 | map_l125_m0_e0 | het | 72.3571 | 66.6667 | 79.1096 | 93.4101 | 230 | 115 | 231 | 61 | 11 | 18.0328 | |
| ciseli-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 49.7009 | 35.0282 | 85.5263 | 70.6564 | 62 | 115 | 65 | 11 | 10 | 90.9091 | |
| ndellapenna-hhga | SNP | * | segdup | * | 99.5371 | 99.5903 | 99.4839 | 89.2221 | 27952 | 115 | 27952 | 145 | 51 | 35.1724 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 74.5853 | 86.8721 | 65.3433 | 69.9161 | 761 | 115 | 609 | 323 | 321 | 99.3808 | |
| qzeng-custom | INDEL | D1_5 | map_l150_m1_e0 | het | 84.3881 | 76.1411 | 94.6387 | 94.4659 | 367 | 115 | 406 | 23 | 19 | 82.6087 | |
| qzeng-custom | SNP | tv | segdup | * | 98.3829 | 98.6521 | 98.1152 | 93.4371 | 8417 | 115 | 8381 | 161 | 27 | 16.7702 | |
| rpoplin-dv42 | INDEL | D6_15 | * | het | 97.5270 | 99.0079 | 96.0896 | 61.5469 | 11477 | 115 | 11451 | 466 | 447 | 95.9227 | |
| raldana-dualsentieon | INDEL | I1_5 | HG002compoundhet | het | 88.2507 | 86.4706 | 90.1055 | 86.0431 | 735 | 115 | 683 | 75 | 74 | 98.6667 | |
| raldana-dualsentieon | INDEL | I6_15 | HG002complexvar | hetalt | 95.1115 | 90.6787 | 100.0000 | 54.5670 | 1109 | 114 | 1149 | 0 | 0 | ||
| gduggal-bwafb | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | het | 41.7658 | 28.7500 | 76.3158 | 69.6000 | 46 | 114 | 58 | 18 | 18 | 100.0000 | |
| gduggal-bwafb | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.4458 | 98.9378 | 97.9586 | 49.7551 | 10618 | 114 | 10653 | 222 | 58 | 26.1261 | |
| gduggal-bwavard | SNP | * | map_l250_m2_e0 | het | 87.1650 | 97.8052 | 78.6127 | 93.0154 | 5080 | 114 | 5032 | 1369 | 34 | 2.4836 | |
| gduggal-bwafb | INDEL | D16_PLUS | HG002compoundhet | het | 83.1185 | 71.8519 | 98.5755 | 24.7427 | 291 | 114 | 1730 | 25 | 25 | 100.0000 | |
| gduggal-bwaplat | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 58.9266 | 44.3902 | 87.6190 | 88.5120 | 91 | 114 | 92 | 13 | 12 | 92.3077 | |
| gduggal-bwaplat | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 58.9266 | 44.3902 | 87.6190 | 88.5120 | 91 | 114 | 92 | 13 | 12 | 92.3077 | |
| gduggal-bwaplat | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 77.6923 | 63.9241 | 99.0196 | 81.1460 | 202 | 114 | 202 | 2 | 2 | 100.0000 | |
| gduggal-bwaplat | SNP | tv | segdup | het | 98.3560 | 97.8438 | 98.8736 | 96.0991 | 5173 | 114 | 5179 | 59 | 6 | 10.1695 | |
| gduggal-bwafb | SNP | tv | map_l125_m0_e0 | * | 98.0737 | 98.2808 | 97.8675 | 77.6619 | 6517 | 114 | 6517 | 142 | 29 | 20.4225 | |
| gduggal-bwafb | SNP | tv | map_l150_m2_e0 | het | 97.9956 | 98.4280 | 97.5670 | 79.8007 | 7138 | 114 | 7138 | 178 | 33 | 18.5393 | |
| gduggal-bwafb | SNP | tv | map_l150_m2_e1 | het | 98.0150 | 98.4486 | 97.5853 | 79.8450 | 7234 | 114 | 7234 | 179 | 33 | 18.4358 | |
| gduggal-bwaplat | INDEL | D1_5 | map_l150_m2_e0 | homalt | 69.1892 | 52.8926 | 100.0000 | 93.1660 | 128 | 114 | 128 | 0 | 0 | ||
| ltrigg-rtg1 | SNP | * | map_siren | homalt | 99.8648 | 99.7933 | 99.9364 | 52.2080 | 55042 | 114 | 55031 | 35 | 31 | 88.5714 | |
| jpowers-varprowl | INDEL | I1_5 | map_l100_m1_e0 | * | 93.9404 | 91.4862 | 96.5300 | 83.1405 | 1225 | 114 | 1224 | 44 | 31 | 70.4545 | |
| dgrover-gatk | SNP | * | map_l125_m1_e0 | homalt | 99.6085 | 99.3256 | 99.8929 | 63.9547 | 16791 | 114 | 16791 | 18 | 13 | 72.2222 | |
| dgrover-gatk | SNP | tv | map_l125_m1_e0 | * | 99.2231 | 99.2882 | 99.1581 | 73.2603 | 15902 | 114 | 15900 | 135 | 27 | 20.0000 | |
| dgrover-gatk | SNP | tv | map_l125_m2_e0 | * | 99.2454 | 99.3086 | 99.1822 | 74.7468 | 16375 | 114 | 16373 | 135 | 27 | 20.0000 | |
| dgrover-gatk | SNP | tv | map_l125_m2_e1 | * | 99.2530 | 99.3156 | 99.1905 | 74.7864 | 16543 | 114 | 16541 | 135 | 27 | 20.0000 | |
| gduggal-snapplat | INDEL | D1_5 | map_l100_m2_e1 | homalt | 88.9945 | 81.6129 | 97.8441 | 87.0712 | 506 | 114 | 590 | 13 | 1 | 7.6923 | |
| gduggal-snapplat | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | het | 10.4575 | 6.5574 | 25.8065 | 80.9816 | 8 | 114 | 8 | 23 | 0 | 0.0000 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | het | 76.6125 | 83.7838 | 70.5720 | 29.6655 | 589 | 114 | 1024 | 427 | 379 | 88.7588 | |
| gduggal-snapfb | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 39.3617 | 24.5033 | 100.0000 | 15.9091 | 37 | 114 | 37 | 0 | 0 | ||