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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
13801-13850 / 86044 show all | |||||||||||||||
| gduggal-bwafb | SNP | * | map_l125_m2_e1 | homalt | 99.4990 | 99.1216 | 99.8793 | 70.3837 | 17378 | 154 | 17378 | 21 | 13 | 61.9048 | |
| gduggal-bwafb | SNP | tv | map_l150_m1_e0 | * | 98.4669 | 98.5887 | 98.3454 | 76.8340 | 10758 | 154 | 10758 | 181 | 38 | 20.9945 | |
| gduggal-bwavard | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 42.0664 | 27.0142 | 95.0000 | 71.0145 | 57 | 154 | 57 | 3 | 3 | 100.0000 | |
| qzeng-custom | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 87.7736 | 89.0780 | 86.5068 | 60.4550 | 1256 | 154 | 2526 | 394 | 302 | 76.6497 | |
| qzeng-custom | INDEL | D1_5 | map_l125_m1_e0 | het | 86.5537 | 78.7879 | 96.0177 | 92.5772 | 572 | 154 | 651 | 27 | 21 | 77.7778 | |
| mlin-fermikit | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 86.4923 | 90.0065 | 83.2423 | 70.9011 | 1387 | 154 | 1371 | 276 | 273 | 98.9130 | |
| mlin-fermikit | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | het | 38.5511 | 68.5714 | 26.8126 | 57.5000 | 336 | 154 | 196 | 535 | 531 | 99.2523 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 91.5762 | 95.2963 | 88.1356 | 47.4691 | 3120 | 154 | 2808 | 378 | 341 | 90.2116 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 87.7109 | 81.5789 | 94.8396 | 65.2279 | 682 | 154 | 680 | 37 | 31 | 83.7838 | |
| ckim-isaac | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 90.7251 | 83.8065 | 98.8889 | 77.1767 | 797 | 154 | 801 | 9 | 7 | 77.7778 | |
| ckim-vqsr | INDEL | * | map_siren | het | 97.3739 | 96.6060 | 98.1540 | 87.1388 | 4355 | 153 | 4360 | 82 | 11 | 13.4146 | |
| egarrison-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.2341 | 97.7771 | 98.6954 | 80.9079 | 6730 | 153 | 6733 | 89 | 29 | 32.5843 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 76.5556 | 82.5342 | 71.3846 | 62.2751 | 723 | 153 | 464 | 186 | 158 | 84.9462 | |
| dgrover-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 98.1938 | 98.9533 | 97.4458 | 67.6938 | 14464 | 153 | 14078 | 369 | 346 | 93.7669 | |
| dgrover-gatk | INDEL | D1_5 | HG002complexvar | * | 99.6498 | 99.5323 | 99.7675 | 58.6672 | 32562 | 153 | 32617 | 76 | 66 | 86.8421 | |
| ciseli-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 44.0468 | 83.2421 | 29.9463 | 79.5867 | 760 | 153 | 781 | 1827 | 29 | 1.5873 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 75.6187 | 75.7143 | 75.5233 | 66.0841 | 477 | 153 | 469 | 152 | 89 | 58.5526 | |
| ckim-gatk | INDEL | * | * | homalt | 99.5712 | 99.8778 | 99.2664 | 58.9388 | 125019 | 153 | 125032 | 924 | 905 | 97.9437 | |
| hfeng-pmm3 | INDEL | I16_PLUS | HG002compoundhet | hetalt | 96.1827 | 92.6899 | 99.9490 | 46.0226 | 1940 | 153 | 1960 | 1 | 1 | 100.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | HG002complexvar | het | 99.5309 | 99.1588 | 99.9057 | 57.5378 | 18036 | 153 | 18015 | 17 | 6 | 35.2941 | |
| hfeng-pmm1 | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | het | 97.5094 | 95.1398 | 100.0000 | 68.6617 | 2995 | 153 | 2995 | 0 | 0 | ||
| gduggal-snapvard | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 82.5113 | 95.2894 | 72.7551 | 82.9109 | 3095 | 153 | 3095 | 1159 | 30 | 2.5884 | |
| gduggal-snapvard | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | * | 4.7019 | 2.5478 | 30.4348 | 66.6667 | 4 | 153 | 7 | 16 | 14 | 87.5000 | |
| jpowers-varprowl | SNP | ti | map_l125_m1_e0 | homalt | 99.2166 | 98.6148 | 99.8259 | 68.6168 | 10892 | 153 | 10892 | 19 | 15 | 78.9474 | |
| jpowers-varprowl | SNP | ti | map_l125_m2_e0 | homalt | 99.2383 | 98.6529 | 99.8307 | 70.9546 | 11205 | 153 | 11205 | 19 | 15 | 78.9474 | |
| jpowers-varprowl | SNP | ti | map_l125_m2_e1 | homalt | 99.2450 | 98.6647 | 99.8322 | 70.9730 | 11305 | 153 | 11305 | 19 | 15 | 78.9474 | |
| jli-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.0932 | 95.6186 | 98.6140 | 50.2202 | 3339 | 153 | 3344 | 47 | 36 | 76.5957 | |
| jmaeng-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 96.9531 | 94.2953 | 99.7651 | 38.9579 | 2529 | 153 | 2548 | 6 | 6 | 100.0000 | |
| astatham-gatk | INDEL | I16_PLUS | HG002compoundhet | hetalt | 96.1827 | 92.6899 | 99.9491 | 45.9080 | 1940 | 153 | 1962 | 1 | 1 | 100.0000 | |
| bgallagher-sentieon | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 99.0051 | 99.4671 | 98.5473 | 71.4531 | 28559 | 153 | 28559 | 421 | 23 | 5.4632 | |
| bgallagher-sentieon | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 99.0051 | 99.4671 | 98.5473 | 71.4531 | 28559 | 153 | 28559 | 421 | 23 | 5.4632 | |
| asubramanian-gatk | INDEL | * | map_l150_m1_e0 | het | 86.9483 | 82.1053 | 92.3984 | 93.4997 | 702 | 153 | 705 | 58 | 6 | 10.3448 | |
| mlin-fermikit | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | * | 96.6168 | 96.8493 | 96.3855 | 66.9947 | 4703 | 153 | 4720 | 177 | 125 | 70.6215 | |
| rpoplin-dv42 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 98.8625 | 98.1712 | 99.5636 | 45.3709 | 8213 | 153 | 8213 | 36 | 34 | 94.4444 | |
| raldana-dualsentieon | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 90.5586 | 84.7305 | 97.2477 | 63.2687 | 849 | 153 | 848 | 24 | 21 | 87.5000 | |
| gduggal-bwavard | SNP | ti | segdup | homalt | 98.7626 | 97.9614 | 99.5771 | 88.2815 | 7352 | 153 | 7300 | 31 | 30 | 96.7742 | |
| eyeh-varpipe | SNP | * | map_l100_m1_e0 | het | 97.9959 | 99.6627 | 96.3839 | 70.0308 | 45206 | 153 | 43739 | 1641 | 34 | 2.0719 | |
| gduggal-bwaplat | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 40.1515 | 25.7282 | 91.3793 | 89.3186 | 53 | 153 | 53 | 5 | 4 | 80.0000 | |
| gduggal-bwafb | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.8088 | 99.1429 | 96.5101 | 64.4371 | 17698 | 153 | 17754 | 642 | 126 | 19.6262 | |
| gduggal-bwafb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 95.3372 | 98.5927 | 92.2897 | 84.7602 | 10649 | 152 | 10677 | 892 | 112 | 12.5561 | |
| gduggal-bwavard | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 36.8928 | 25.8537 | 64.3836 | 82.9837 | 53 | 152 | 47 | 26 | 1 | 3.8462 | |
| gduggal-bwavard | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 36.8928 | 25.8537 | 64.3836 | 82.9837 | 53 | 152 | 47 | 26 | 1 | 3.8462 | |
| gduggal-bwavard | SNP | tv | map_l125_m0_e0 | * | 92.0149 | 97.7077 | 86.9489 | 82.9272 | 6479 | 152 | 6469 | 971 | 34 | 3.5015 | |
| gduggal-bwaplat | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 70.6542 | 55.4252 | 97.4227 | 64.6630 | 189 | 152 | 189 | 5 | 5 | 100.0000 | |
| gduggal-bwaplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 58.5323 | 47.2222 | 76.9663 | 86.5964 | 136 | 152 | 137 | 41 | 3 | 7.3171 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.5010 | 99.4006 | 99.6016 | 52.3483 | 25207 | 152 | 26749 | 107 | 95 | 88.7850 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 69.0901 | 55.6851 | 90.9953 | 55.8577 | 191 | 152 | 192 | 19 | 18 | 94.7368 | |
| jli-custom | SNP | tv | map_l125_m2_e0 | * | 99.2648 | 99.0782 | 99.4521 | 69.0688 | 16337 | 152 | 16336 | 90 | 26 | 28.8889 | |
| jli-custom | SNP | tv | map_l125_m2_e1 | * | 99.2722 | 99.0875 | 99.4576 | 69.1406 | 16505 | 152 | 16504 | 90 | 26 | 28.8889 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | * | 87.5391 | 79.3197 | 97.6589 | 50.7414 | 583 | 152 | 584 | 14 | 14 | 100.0000 | |