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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
56851-56900 / 86044 show all | |||||||||||||||
| jli-custom | INDEL | * | tech_badpromoters | * | 97.9866 | 96.0526 | 100.0000 | 53.7975 | 73 | 3 | 73 | 0 | 0 | ||
| jlack-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 98.8869 | 98.7135 | 99.0610 | 53.7961 | 844 | 11 | 844 | 8 | 0 | 0.0000 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.7471 | 99.5042 | 99.9911 | 53.7923 | 11240 | 56 | 11209 | 1 | 1 | 100.0000 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 51.1480 | 34.9051 | 95.6654 | 53.7872 | 2813 | 5246 | 2825 | 128 | 108 | 84.3750 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 51.1480 | 34.9051 | 95.6654 | 53.7872 | 2813 | 5246 | 2825 | 128 | 108 | 84.3750 | |
| ckim-isaac | SNP | * | map_siren | het | 87.0731 | 77.2065 | 99.8309 | 53.7836 | 70251 | 20740 | 70263 | 119 | 18 | 15.1261 | |
| gduggal-snapfb | INDEL | D6_15 | HG002complexvar | homalt | 79.2659 | 75.0214 | 84.0196 | 53.7834 | 877 | 292 | 857 | 163 | 160 | 98.1595 | |
| raldana-dualsentieon | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 74.0331 | 94.3662 | 60.9091 | 53.7815 | 67 | 4 | 67 | 43 | 43 | 100.0000 | |
| gduggal-bwafb | INDEL | D6_15 | HG002complexvar | * | 93.2387 | 90.0604 | 96.6496 | 53.7803 | 4775 | 527 | 4904 | 170 | 143 | 84.1176 | |
| ltrigg-rtg1 | INDEL | I16_PLUS | HG002complexvar | homalt | 95.1273 | 94.1748 | 96.0993 | 53.7705 | 291 | 18 | 271 | 11 | 11 | 100.0000 | |
| mlin-fermikit | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 65.2028 | 60.0760 | 71.2862 | 53.7688 | 790 | 525 | 787 | 317 | 306 | 96.5300 | |
| gduggal-bwafb | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 79.4509 | 70.3322 | 91.2863 | 53.7682 | 2456 | 1036 | 1540 | 147 | 142 | 96.5986 | |
| ndellapenna-hhga | INDEL | I1_5 | HG002complexvar | * | 98.8448 | 98.3844 | 99.3095 | 53.7677 | 32824 | 539 | 32792 | 228 | 116 | 50.8772 | |
| jli-custom | INDEL | I16_PLUS | * | hetalt | 96.3839 | 93.3270 | 99.6479 | 53.7674 | 1958 | 140 | 1981 | 7 | 7 | 100.0000 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 59.1721 | 54.4401 | 64.8052 | 53.7673 | 8736 | 7311 | 8947 | 4859 | 4228 | 87.0138 | |
| ltrigg-rtg2 | SNP | * | map_l100_m0_e0 | * | 98.7191 | 97.6280 | 99.8350 | 53.7664 | 32062 | 779 | 32065 | 53 | 9 | 16.9811 | |
| ciseli-custom | SNP | tv | HG002compoundhet | het | 56.8474 | 77.9585 | 44.7336 | 53.7648 | 3643 | 1030 | 3678 | 4544 | 89 | 1.9586 | |
| hfeng-pmm2 | INDEL | D6_15 | func_cds | * | 100.0000 | 100.0000 | 100.0000 | 53.7634 | 43 | 0 | 43 | 0 | 0 | ||
| mlin-fermikit | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.5545 | 99.7340 | 97.4026 | 53.7630 | 1125 | 3 | 1125 | 30 | 23 | 76.6667 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 68.7500 | 83.7563 | 58.3039 | 53.7582 | 165 | 32 | 165 | 118 | 105 | 88.9831 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 45.2414 | 29.6315 | 95.6081 | 53.7572 | 2388 | 5671 | 2830 | 130 | 123 | 94.6154 | |
| rpoplin-dv42 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.8959 | 99.7921 | 100.0000 | 53.7572 | 480 | 1 | 480 | 0 | 0 | ||
| eyeh-varpipe | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 45.2414 | 29.6315 | 95.6081 | 53.7572 | 2388 | 5671 | 2830 | 130 | 123 | 94.6154 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 94.1056 | 96.6465 | 91.6950 | 53.7560 | 3516 | 122 | 3511 | 318 | 204 | 64.1509 | |
| gduggal-bwaplat | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 79.5052 | 66.5627 | 98.6958 | 53.7549 | 2347 | 1179 | 2346 | 31 | 28 | 90.3226 | |
| gduggal-bwaplat | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 79.5052 | 66.5627 | 98.6958 | 53.7549 | 2347 | 1179 | 2346 | 31 | 28 | 90.3226 | |
| hfeng-pmm3 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.6756 | 99.3855 | 99.9675 | 53.7536 | 6146 | 38 | 6146 | 2 | 0 | 0.0000 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | het | 80.2269 | 68.5786 | 96.6418 | 53.7532 | 275 | 126 | 518 | 18 | 17 | 94.4444 | |
| eyeh-varpipe | SNP | tv | tech_badpromoters | homalt | 100.0000 | 100.0000 | 100.0000 | 53.7500 | 39 | 0 | 37 | 0 | 0 | ||
| jpowers-varprowl | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | het | 37.1767 | 79.2899 | 24.2806 | 53.7438 | 134 | 35 | 135 | 421 | 420 | 99.7625 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.3971 | 97.0646 | 97.7319 | 53.7356 | 14351 | 434 | 14349 | 333 | 323 | 96.9970 | |
| ghariani-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 59.0686 | 94.1575 | 43.0321 | 53.7351 | 13763 | 854 | 13840 | 18322 | 18101 | 98.7938 | |
| egarrison-hhga | INDEL | D6_15 | * | * | 86.6592 | 82.4007 | 91.3819 | 53.7350 | 21500 | 4592 | 21631 | 2040 | 1771 | 86.8137 | |
| gduggal-bwavard | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 97.6712 | 95.6754 | 99.7520 | 53.7159 | 1615 | 73 | 1609 | 4 | 3 | 75.0000 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 92.4855 | 86.9565 | 98.7654 | 53.7143 | 80 | 12 | 80 | 1 | 0 | 0.0000 | |
| ckim-isaac | SNP | * | map_l100_m0_e0 | homalt | 67.7175 | 51.2048 | 99.9496 | 53.7128 | 5950 | 5670 | 5950 | 3 | 3 | 100.0000 | |
| ltrigg-rtg2 | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 99.5230 | 99.3610 | 99.6855 | 53.7118 | 311 | 2 | 317 | 1 | 1 | 100.0000 | |
| raldana-dualsentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 97.9826 | 99.7269 | 96.2982 | 53.7111 | 9495 | 26 | 9495 | 365 | 360 | 98.6301 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 92.8302 | 90.7619 | 94.9950 | 53.7071 | 953 | 97 | 949 | 50 | 49 | 98.0000 | |
| rpoplin-dv42 | INDEL | I16_PLUS | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 92.3077 | 85.7143 | 100.0000 | 53.7037 | 24 | 4 | 25 | 0 | 0 | ||
| ltrigg-rtg2 | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 98.1641 | 97.2350 | 99.1111 | 53.7037 | 211 | 6 | 223 | 2 | 2 | 100.0000 | |
| jpowers-varprowl | INDEL | I6_15 | HG002compoundhet | homalt | 11.4804 | 61.2903 | 6.3333 | 53.7037 | 19 | 12 | 19 | 281 | 260 | 92.5267 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.0354 | 98.0892 | 100.0000 | 53.7037 | 154 | 3 | 150 | 0 | 0 | ||
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_51to200 | * | 96.0000 | 96.0000 | 96.0000 | 53.7037 | 24 | 1 | 24 | 1 | 0 | 0.0000 | |
| jpowers-varprowl | INDEL | * | tech_badpromoters | * | 74.4828 | 71.0526 | 78.2609 | 53.6913 | 54 | 22 | 54 | 15 | 15 | 100.0000 | |
| jli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 98.9179 | 98.5780 | 99.2602 | 53.6895 | 7279 | 105 | 7245 | 54 | 49 | 90.7407 | |
| mlin-fermikit | INDEL | I16_PLUS | HG002compoundhet | * | 58.0506 | 50.3033 | 68.6187 | 53.6851 | 1078 | 1065 | 1078 | 493 | 492 | 99.7972 | |
| ghariani-varprowl | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 53.5870 | 96.7318 | 37.0581 | 53.6813 | 3167 | 107 | 3187 | 5413 | 5386 | 99.5012 | |
| mlin-fermikit | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 88.2321 | 85.5737 | 91.0609 | 53.6742 | 26877 | 4531 | 26832 | 2634 | 2540 | 96.4313 | |
| mlin-fermikit | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 88.2321 | 85.5737 | 91.0609 | 53.6742 | 26877 | 4531 | 26832 | 2634 | 2540 | 96.4313 | |