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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
73201-73250 / 86044 show all | |||||||||||||||
| gduggal-bwaplat | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 87.1106 | 77.9126 | 98.7711 | 74.0431 | 642 | 182 | 643 | 8 | 2 | 25.0000 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 79.4291 | 78.9108 | 79.9542 | 56.7822 | 681 | 182 | 698 | 175 | 172 | 98.2857 | |
| gduggal-bwavard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 97.5038 | 95.3512 | 99.7559 | 75.0693 | 3733 | 182 | 3678 | 9 | 6 | 66.6667 | |
| eyeh-varpipe | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 66.9909 | 56.2201 | 82.8667 | 28.6733 | 235 | 183 | 1243 | 257 | 257 | 100.0000 | |
| gduggal-bwafb | SNP | tv | map_l125_m2_e0 | * | 98.6658 | 98.8902 | 98.4424 | 74.7627 | 16306 | 183 | 16306 | 258 | 51 | 19.7674 | |
| gduggal-bwafb | SNP | tv | map_l125_m2_e1 | * | 98.6792 | 98.9014 | 98.4580 | 74.8361 | 16474 | 183 | 16474 | 258 | 51 | 19.7674 | |
| gduggal-bwaplat | INDEL | * | map_l150_m0_e0 | het | 63.2000 | 46.3343 | 99.3711 | 97.9552 | 158 | 183 | 158 | 1 | 0 | 0.0000 | |
| raldana-dualsentieon | SNP | * | map_l150_m0_e0 | * | 98.5116 | 98.4791 | 98.5442 | 78.4632 | 11849 | 183 | 11846 | 175 | 7 | 4.0000 | |
| ltrigg-rtg2 | INDEL | * | HG002compoundhet | het | 95.9824 | 95.5300 | 96.4390 | 67.6682 | 3911 | 183 | 3954 | 146 | 79 | 54.1096 | |
| ltrigg-rtg2 | INDEL | * | map_siren | * | 98.2573 | 97.5304 | 98.9952 | 77.5300 | 7227 | 183 | 7192 | 73 | 11 | 15.0685 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 87.0329 | 82.8169 | 91.7012 | 56.1220 | 882 | 183 | 884 | 80 | 65 | 81.2500 | |
| ckim-isaac | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 68.0484 | 51.8421 | 98.9950 | 48.4456 | 197 | 183 | 197 | 2 | 2 | 100.0000 | |
| ckim-isaac | INDEL | I1_5 | map_l100_m2_e1 | homalt | 79.1574 | 66.1111 | 98.6188 | 77.9671 | 357 | 183 | 357 | 5 | 2 | 40.0000 | |
| gduggal-snapfb | SNP | tv | map_l100_m0_e0 | het | 95.8604 | 97.4661 | 94.3068 | 70.6611 | 7039 | 183 | 7040 | 425 | 163 | 38.3529 | |
| gduggal-snapfb | SNP | tv | map_l150_m2_e0 | het | 95.8184 | 97.4766 | 94.2156 | 77.2326 | 7069 | 183 | 7069 | 434 | 174 | 40.0922 | |
| gduggal-snapvard | INDEL | D6_15 | map_siren | * | 67.5902 | 64.0472 | 71.5481 | 80.9182 | 326 | 183 | 342 | 136 | 91 | 66.9118 | |
| gduggal-snapvard | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 55.0228 | 69.6517 | 45.4722 | 29.4037 | 420 | 183 | 1868 | 2240 | 2137 | 95.4018 | |
| anovak-vg | INDEL | * | map_l125_m0_e0 | het | 70.2289 | 68.8245 | 71.6918 | 91.8286 | 404 | 183 | 428 | 169 | 55 | 32.5444 | |
| anovak-vg | INDEL | I1_5 | map_l150_m2_e1 | het | 50.9949 | 42.2713 | 64.2553 | 93.6383 | 134 | 183 | 151 | 84 | 8 | 9.5238 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 93.6118 | 90.0651 | 97.4492 | 65.8974 | 1659 | 183 | 1872 | 49 | 41 | 83.6735 | |
| jli-custom | INDEL | * | * | homalt | 99.7041 | 99.8538 | 99.5548 | 57.2311 | 124989 | 183 | 124999 | 559 | 535 | 95.7066 | |
| ckim-dragen | INDEL | I16_PLUS | HG002compoundhet | hetalt | 95.4049 | 91.2566 | 99.9482 | 45.8824 | 1910 | 183 | 1931 | 1 | 1 | 100.0000 | |
| ckim-dragen | SNP | * | map_l250_m2_e0 | * | 97.2970 | 97.6791 | 96.9179 | 89.7648 | 7702 | 183 | 7704 | 245 | 31 | 12.6531 | |
| ckim-dragen | SNP | ti | map_l125_m2_e0 | het | 97.7337 | 99.0305 | 96.4704 | 78.2642 | 18693 | 183 | 18695 | 684 | 65 | 9.5029 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 82.3222 | 88.6547 | 76.8340 | 52.5393 | 1430 | 183 | 1393 | 420 | 417 | 99.2857 | |
| mlin-fermikit | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 95.9291 | 98.9219 | 93.1120 | 72.4097 | 16792 | 183 | 16803 | 1243 | 1086 | 87.3693 | |
| mlin-fermikit | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 95.9291 | 98.9219 | 93.1120 | 72.4097 | 16792 | 183 | 16803 | 1243 | 1086 | 87.3693 | |
| ndellapenna-hhga | SNP | tv | map_l100_m0_e0 | * | 98.9920 | 98.3490 | 99.6435 | 65.9868 | 10901 | 183 | 10901 | 39 | 17 | 43.5897 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 93.2033 | 94.2180 | 92.2102 | 45.7942 | 2982 | 183 | 2983 | 252 | 219 | 86.9048 | |
| ltrigg-rtg2 | INDEL | D16_PLUS | HG002compoundhet | * | 95.5047 | 92.1828 | 99.0749 | 28.5997 | 2158 | 183 | 2142 | 20 | 20 | 100.0000 | |
| ltrigg-rtg2 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 91.7092 | 86.1153 | 98.0803 | 52.6837 | 1135 | 183 | 1124 | 22 | 22 | 100.0000 | |
| ltrigg-rtg2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 98.4378 | 97.3195 | 99.5821 | 32.8253 | 6644 | 183 | 6672 | 28 | 28 | 100.0000 | |
| mlin-fermikit | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | * | 95.5288 | 96.1960 | 94.8708 | 69.9124 | 4653 | 184 | 4661 | 252 | 157 | 62.3016 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 64.1239 | 47.4286 | 98.9583 | 48.3871 | 166 | 184 | 190 | 2 | 1 | 50.0000 | |
| ndellapenna-hhga | SNP | tv | HG002complexvar | homalt | 99.8464 | 99.8065 | 99.8864 | 22.8760 | 94927 | 184 | 94935 | 108 | 97 | 89.8148 | |
| ndellapenna-hhga | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.3259 | 98.9526 | 99.7019 | 63.0961 | 17384 | 184 | 17391 | 52 | 20 | 38.4615 | |
| gduggal-snapvard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 58.8714 | 87.8468 | 44.2696 | 89.1685 | 1330 | 184 | 1294 | 1629 | 74 | 4.5427 | |
| gduggal-snapplat | INDEL | I1_5 | map_l125_m2_e1 | * | 84.0458 | 78.8506 | 89.9740 | 94.0271 | 686 | 184 | 691 | 77 | 4 | 5.1948 | |
| gduggal-snapplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 86.6794 | 93.1497 | 81.0496 | 83.5702 | 2502 | 184 | 2502 | 585 | 8 | 1.3675 | |
| gduggal-snapfb | SNP | tv | map_l150_m2_e1 | het | 95.8395 | 97.4959 | 94.2384 | 77.2735 | 7164 | 184 | 7164 | 438 | 174 | 39.7260 | |
| gduggal-snapvard | INDEL | * | map_l100_m1_e0 | homalt | 91.2452 | 85.0041 | 98.4754 | 75.7601 | 1043 | 184 | 1421 | 22 | 18 | 81.8182 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 72.4442 | 68.0556 | 77.4379 | 54.5217 | 392 | 184 | 405 | 118 | 115 | 97.4576 | |
| gduggal-bwaplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 80.5781 | 70.7937 | 93.5010 | 80.1167 | 446 | 184 | 446 | 31 | 9 | 29.0323 | |
| gduggal-bwafb | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 18.4100 | 10.6796 | 66.6667 | 69.1589 | 22 | 184 | 22 | 11 | 10 | 90.9091 | |
| gduggal-bwafb | SNP | * | map_l100_m1_e0 | homalt | 99.5971 | 99.3186 | 99.8771 | 62.3452 | 26819 | 184 | 26819 | 33 | 19 | 57.5758 | |
| gduggal-bwavard | SNP | * | func_cds | * | 99.3111 | 98.9862 | 99.6380 | 30.1556 | 17966 | 184 | 17892 | 65 | 23 | 35.3846 | |
| gduggal-bwavard | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 98.7554 | 98.3399 | 99.1744 | 57.4612 | 10900 | 184 | 10811 | 90 | 55 | 61.1111 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 91.9839 | 85.7475 | 99.1986 | 31.0197 | 1107 | 184 | 1114 | 9 | 9 | 100.0000 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 94.4844 | 97.2451 | 91.8762 | 38.9766 | 6495 | 184 | 6322 | 559 | 498 | 89.0877 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.7426 | 96.1442 | 99.3950 | 25.7739 | 4588 | 184 | 4600 | 28 | 27 | 96.4286 | |