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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
18351-18400 / 86044 show all | |||||||||||||||
| ciseli-custom | INDEL | * | map_l125_m1_e0 | * | 67.4524 | 62.0788 | 73.8444 | 90.3002 | 1308 | 799 | 1310 | 464 | 300 | 64.6552 | |
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 95.4904 | 92.7660 | 98.3796 | 71.9905 | 1308 | 102 | 1275 | 21 | 12 | 57.1429 | |
| egarrison-hhga | INDEL | D16_PLUS | HG002complexvar | * | 85.7883 | 79.5496 | 93.0889 | 62.2772 | 1307 | 336 | 1320 | 98 | 72 | 73.4694 | |
| ckim-isaac | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 96.7794 | 94.2322 | 99.4681 | 58.4858 | 1307 | 80 | 1309 | 7 | 1 | 14.2857 | |
| egarrison-hhga | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.8472 | 99.6949 | 100.0000 | 35.4886 | 1307 | 4 | 1307 | 0 | 0 | ||
| astatham-gatk | SNP | * | map_l250_m0_e0 | het | 92.0747 | 86.7862 | 98.0495 | 94.4847 | 1307 | 199 | 1307 | 26 | 3 | 11.5385 | |
| ckim-dragen | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.8472 | 99.6949 | 100.0000 | 33.7893 | 1307 | 4 | 1307 | 0 | 0 | ||
| ghariani-varprowl | INDEL | * | map_l125_m1_e0 | het | 91.1754 | 97.9026 | 85.3133 | 91.4837 | 1307 | 28 | 1307 | 225 | 73 | 32.4444 | |
| raldana-dualsentieon | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 94.8453 | 92.6241 | 97.1756 | 71.4036 | 1306 | 104 | 1273 | 37 | 32 | 86.4865 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.8615 | 98.0480 | 99.6885 | 70.4692 | 1306 | 26 | 1280 | 4 | 2 | 50.0000 | |
| mlin-fermikit | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 98.3434 | 99.6186 | 97.1004 | 38.0755 | 1306 | 5 | 1306 | 39 | 35 | 89.7436 | |
| raldana-dualsentieon | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 95.3947 | 91.7722 | 99.3151 | 87.7368 | 1305 | 117 | 1305 | 9 | 7 | 77.7778 | |
| jmaeng-gatk | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.7706 | 99.5423 | 100.0000 | 34.4550 | 1305 | 6 | 1305 | 0 | 0 | ||
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 96.4907 | 96.3100 | 96.6721 | 79.6867 | 1305 | 50 | 1191 | 41 | 29 | 70.7317 | |
| astatham-gatk | INDEL | * | map_l125_m2_e1 | het | 94.9130 | 92.6847 | 97.2511 | 89.9694 | 1305 | 103 | 1309 | 37 | 5 | 13.5135 | |
| ciseli-custom | INDEL | * | HG002compoundhet | het | 30.5417 | 31.9071 | 29.2883 | 74.6335 | 1305 | 2785 | 2889 | 6975 | 4438 | 63.6272 | |
| ckim-gatk | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.7706 | 99.5423 | 100.0000 | 34.5537 | 1305 | 6 | 1305 | 0 | 0 | ||
| ciseli-custom | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 96.7002 | 99.5423 | 94.0159 | 40.8529 | 1305 | 6 | 1304 | 83 | 22 | 26.5060 | |
| cchapple-custom | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.7323 | 99.4661 | 100.0000 | 30.4021 | 1304 | 7 | 1298 | 0 | 0 | ||
| mlin-fermikit | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.4225 | 97.6048 | 97.2409 | 55.7572 | 1304 | 32 | 1304 | 37 | 14 | 37.8378 | |
| gduggal-bwafb | SNP | tv | map_l150_m0_e0 | homalt | 99.0129 | 98.1928 | 99.8469 | 80.0489 | 1304 | 24 | 1304 | 2 | 2 | 100.0000 | |
| gduggal-bwaplat | INDEL | * | segdup | het | 93.7455 | 88.9495 | 99.0881 | 97.0073 | 1304 | 162 | 1304 | 12 | 6 | 50.0000 | |
| gduggal-bwaplat | INDEL | D16_PLUS | * | hetalt | 80.2709 | 67.4599 | 99.0881 | 50.5635 | 1304 | 629 | 1304 | 12 | 11 | 91.6667 | |
| egarrison-hhga | INDEL | * | map_l125_m1_e0 | het | 97.6831 | 97.6779 | 97.6883 | 86.3886 | 1304 | 31 | 1310 | 31 | 10 | 32.2581 | |
| astatham-gatk | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.7323 | 99.4661 | 100.0000 | 34.5710 | 1304 | 7 | 1304 | 0 | 0 | ||
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.7467 | 97.8979 | 99.6103 | 71.3232 | 1304 | 28 | 1278 | 5 | 4 | 80.0000 | |
| mlin-fermikit | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 98.0394 | 97.9699 | 98.1089 | 39.1064 | 1303 | 27 | 1297 | 25 | 25 | 100.0000 | |
| rpoplin-dv42 | INDEL | * | map_l150_m1_e0 | * | 97.8620 | 97.3842 | 98.3446 | 98.9844 | 1303 | 35 | 1307 | 22 | 10 | 45.4545 | |
| ciseli-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 84.1283 | 97.5299 | 73.9648 | 66.0177 | 1303 | 33 | 1304 | 459 | 12 | 2.6144 | |
| gduggal-snapplat | INDEL | I1_5 | map_siren | het | 80.2443 | 77.5134 | 83.1746 | 91.4579 | 1303 | 378 | 1310 | 265 | 10 | 3.7736 | |
| asubramanian-gatk | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.6940 | 99.3898 | 100.0000 | 34.8326 | 1303 | 8 | 1304 | 0 | 0 | ||
| egarrison-hhga | INDEL | * | map_l150_m1_e0 | * | 97.6046 | 97.3842 | 97.8261 | 98.6310 | 1303 | 35 | 1305 | 29 | 10 | 34.4828 | |
| ckim-vqsr | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.6556 | 99.3135 | 100.0000 | 34.6057 | 1302 | 9 | 1302 | 0 | 0 | ||
| ndellapenna-hhga | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 64.5816 | 61.9705 | 67.4224 | 73.1294 | 1302 | 799 | 1368 | 661 | 606 | 91.6793 | |
| gduggal-bwaplat | INDEL | D16_PLUS | HG002compoundhet | hetalt | 80.5942 | 67.5311 | 99.9233 | 34.2251 | 1302 | 626 | 1302 | 1 | 1 | 100.0000 | |
| gduggal-bwaplat | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 80.2465 | 67.4262 | 99.0868 | 50.5085 | 1302 | 629 | 1302 | 12 | 11 | 91.6667 | |
| gduggal-bwaplat | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 80.2465 | 67.4262 | 99.0868 | 50.5085 | 1302 | 629 | 1302 | 12 | 11 | 91.6667 | |
| gduggal-snapfb | INDEL | * | map_l150_m2_e0 | * | 93.6073 | 92.4716 | 94.7712 | 89.9313 | 1302 | 106 | 1305 | 72 | 21 | 29.1667 | |
| hfeng-pmm1 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 92.2750 | 85.9974 | 99.5413 | 87.6183 | 1302 | 212 | 1302 | 6 | 4 | 66.6667 | |
| hfeng-pmm3 | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 96.6892 | 96.0886 | 97.2973 | 79.6160 | 1302 | 53 | 1188 | 33 | 29 | 87.8788 | |
| anovak-vg | SNP | ti | map_l250_m2_e0 | homalt | 85.1522 | 74.4425 | 99.4611 | 88.0122 | 1302 | 447 | 1292 | 7 | 5 | 71.4286 | |
| gduggal-snapvard | INDEL | I1_5 | map_l100_m2_e1 | * | 90.6674 | 93.3333 | 88.1496 | 86.2733 | 1302 | 93 | 1815 | 244 | 114 | 46.7213 | |
| gduggal-snapvard | INDEL | * | map_l150_m2_e0 | * | 85.1445 | 92.4716 | 78.8934 | 90.8735 | 1302 | 106 | 1768 | 473 | 151 | 31.9239 | |
| ndellapenna-hhga | INDEL | * | map_l150_m1_e0 | * | 97.6748 | 97.2347 | 98.1189 | 98.7054 | 1301 | 37 | 1304 | 25 | 9 | 36.0000 | |
| cchapple-custom | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 96.6415 | 96.0148 | 97.2764 | 66.3029 | 1301 | 54 | 2643 | 74 | 62 | 83.7838 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.0861 | 98.4860 | 99.6935 | 62.3159 | 1301 | 20 | 1301 | 4 | 2 | 50.0000 | |
| astatham-gatk | SNP | tv | map_l150_m0_e0 | homalt | 98.8226 | 97.9669 | 99.6935 | 75.2231 | 1301 | 27 | 1301 | 4 | 3 | 75.0000 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 95.4016 | 92.2695 | 98.7539 | 72.0200 | 1301 | 109 | 1268 | 16 | 9 | 56.2500 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 92.5616 | 97.8195 | 87.8400 | 82.6726 | 1301 | 29 | 1098 | 152 | 125 | 82.2368 | |
| hfeng-pmm1 | INDEL | D1_5 | HG002complexvar | hetalt | 97.9678 | 96.1538 | 99.8514 | 73.2565 | 1300 | 52 | 1344 | 2 | 1 | 50.0000 | |