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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
75251-75300 / 86044 show all | |||||||||||||||
| egarrison-hhga | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.9850 | 98.7098 | 99.2618 | 74.4815 | 14383 | 188 | 14387 | 107 | 31 | 28.9720 | |
| ckim-vqsr | INDEL | D1_5 | HG002compoundhet | het | 96.1223 | 98.2639 | 94.0720 | 78.9357 | 1698 | 30 | 1698 | 107 | 105 | 98.1308 | |
| jpowers-varprowl | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 77.8551 | 92.7602 | 67.0769 | 92.6287 | 205 | 16 | 218 | 107 | 21 | 19.6262 | |
| jmaeng-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 96.0352 | 98.6256 | 93.5774 | 85.8273 | 1794 | 25 | 1559 | 107 | 85 | 79.4393 | |
| jmaeng-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 96.0352 | 98.6256 | 93.5774 | 85.8273 | 1794 | 25 | 1559 | 107 | 85 | 79.4393 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 88.0678 | 85.5096 | 90.7838 | 68.5024 | 1074 | 182 | 1054 | 107 | 48 | 44.8598 | |
| ckim-isaac | INDEL | * | map_siren | * | 85.3582 | 75.5331 | 98.1215 | 78.4772 | 5597 | 1813 | 5589 | 107 | 46 | 42.9907 | |
| ckim-dragen | INDEL | * | map_l100_m2_e0 | het | 96.2796 | 97.1391 | 95.4352 | 88.1801 | 2241 | 66 | 2237 | 107 | 9 | 8.4112 | |
| cchapple-custom | INDEL | D6_15 | HG002complexvar | * | 96.6422 | 95.3791 | 97.9391 | 52.4803 | 5057 | 245 | 5085 | 107 | 98 | 91.5888 | |
| ckim-gatk | INDEL | D1_5 | HG002compoundhet | het | 96.2104 | 98.4375 | 94.0819 | 78.9081 | 1701 | 27 | 1701 | 107 | 105 | 98.1308 | |
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 95.9408 | 94.7790 | 97.1314 | 64.3062 | 3667 | 202 | 3623 | 107 | 103 | 96.2617 | |
| hfeng-pmm1 | SNP | * | map_l150_m2_e0 | het | 99.1127 | 98.7632 | 99.4646 | 75.9700 | 19884 | 249 | 19878 | 107 | 27 | 25.2336 | |
| hfeng-pmm2 | SNP | tv | map_l150_m1_e0 | het | 98.7581 | 99.0498 | 98.4681 | 78.5736 | 6880 | 66 | 6878 | 107 | 10 | 9.3458 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.1846 | 98.5457 | 99.8318 | 70.9620 | 63494 | 937 | 63506 | 107 | 86 | 80.3738 | |
| ghariani-varprowl | INDEL | D1_5 | segdup | * | 91.2316 | 92.0218 | 90.4550 | 95.5776 | 1015 | 88 | 1014 | 107 | 65 | 60.7477 | |
| gduggal-snapplat | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 88.2507 | 80.5274 | 97.6127 | 83.3538 | 4367 | 1056 | 4375 | 107 | 45 | 42.0561 | |
| gduggal-snapplat | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 88.2507 | 80.5274 | 97.6127 | 83.3538 | 4367 | 1056 | 4375 | 107 | 45 | 42.0561 | |
| gduggal-snapvard | INDEL | * | HG002compoundhet | homalt | 74.7625 | 67.9300 | 83.1230 | 59.6178 | 466 | 220 | 527 | 107 | 96 | 89.7196 | |
| gduggal-snapfb | SNP | * | lowcmp_SimpleRepeat_triTR_51to200 | het | 8.5470 | 100.0000 | 4.4643 | 79.8923 | 7 | 0 | 5 | 107 | 2 | 1.8692 | |
| gduggal-snapplat | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 35.8000 | 22.6696 | 85.0767 | 69.9119 | 608 | 2074 | 610 | 107 | 84 | 78.5047 | |
| ghariani-varprowl | INDEL | D6_15 | map_siren | * | 75.5337 | 73.4774 | 77.7083 | 86.7293 | 374 | 135 | 373 | 107 | 94 | 87.8505 | |
| ghariani-varprowl | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 95.7049 | 99.1018 | 92.5331 | 67.6378 | 1324 | 12 | 1326 | 107 | 8 | 7.4766 | |
| ghariani-varprowl | SNP | ti | map_l250_m0_e0 | het | 93.0734 | 97.1092 | 89.3596 | 95.1651 | 907 | 27 | 907 | 108 | 15 | 13.8889 | |
| hfeng-pmm1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 92.5787 | 91.0009 | 94.2122 | 75.0968 | 1982 | 196 | 1758 | 108 | 96 | 88.8889 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 85.8383 | 78.3200 | 94.9533 | 28.7854 | 6340 | 1755 | 2032 | 108 | 63 | 58.3333 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 74.5911 | 64.9460 | 87.6005 | 39.3454 | 5234 | 2825 | 763 | 108 | 107 | 99.0741 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 74.5911 | 64.9460 | 87.6005 | 39.3454 | 5234 | 2825 | 763 | 108 | 107 | 99.0741 | |
| gduggal-snapfb | INDEL | I6_15 | HG002compoundhet | hetalt | 70.7588 | 57.7252 | 91.3944 | 38.7805 | 4928 | 3609 | 1147 | 108 | 105 | 97.2222 | |
| gduggal-snapplat | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 86.1010 | 77.3614 | 97.0668 | 59.1479 | 3571 | 1045 | 3574 | 108 | 9 | 8.3333 | |
| dgrover-gatk | SNP | tv | map_l100_m0_e0 | het | 98.8895 | 99.2661 | 98.5157 | 76.1747 | 7169 | 53 | 7168 | 108 | 20 | 18.5185 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 67.4035 | 79.2818 | 58.6207 | 66.4093 | 287 | 75 | 153 | 108 | 102 | 94.4444 | |
| ckim-isaac | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.2969 | 92.1490 | 96.5473 | 61.2007 | 2993 | 255 | 3020 | 108 | 27 | 25.0000 | |
| egarrison-hhga | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.3239 | 99.0379 | 99.6116 | 52.2441 | 27690 | 269 | 27695 | 108 | 53 | 49.0741 | |
| eyeh-varpipe | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 75.7444 | 68.4857 | 84.7242 | 61.9892 | 502 | 231 | 599 | 108 | 100 | 92.5926 | |
| ndellapenna-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 76.2491 | 62.1404 | 98.6463 | 36.1300 | 8553 | 5211 | 7870 | 108 | 94 | 87.0370 | |
| ndellapenna-hhga | SNP | tv | HG002complexvar | homalt | 99.8464 | 99.8065 | 99.8864 | 22.8760 | 94927 | 184 | 94935 | 108 | 97 | 89.8148 | |
| qzeng-custom | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | het | 97.4871 | 98.2529 | 96.7332 | 77.3918 | 3093 | 55 | 3198 | 108 | 35 | 32.4074 | |
| qzeng-custom | SNP | ti | map_l250_m0_e0 | het | 67.5985 | 56.9593 | 83.1250 | 98.4261 | 532 | 402 | 532 | 108 | 85 | 78.7037 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 71.5746 | 78.1250 | 66.0377 | 64.7450 | 225 | 63 | 210 | 108 | 106 | 98.1481 | |
| qzeng-custom | INDEL | D6_15 | HG002complexvar | homalt | 94.3279 | 97.3482 | 91.4894 | 56.3918 | 1138 | 31 | 1161 | 108 | 53 | 49.0741 | |
| qzeng-custom | INDEL | D6_15 | map_l100_m1_e0 | * | 77.6887 | 86.0465 | 70.8108 | 85.0746 | 222 | 36 | 262 | 108 | 10 | 9.2593 | |
| raldana-dualsentieon | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 97.9616 | 97.0020 | 98.9403 | 47.2355 | 10095 | 312 | 10084 | 108 | 100 | 92.5926 | |
| raldana-dualsentieon | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.2190 | 99.9172 | 98.5304 | 36.2675 | 7241 | 6 | 7241 | 108 | 107 | 99.0741 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 92.8572 | 96.8783 | 89.1566 | 74.3497 | 931 | 30 | 888 | 108 | 98 | 90.7407 | |
| anovak-vg | INDEL | I6_15 | map_siren | * | 52.3607 | 48.1967 | 57.3123 | 74.7000 | 147 | 158 | 145 | 108 | 71 | 65.7407 | |
| asubramanian-gatk | INDEL | D1_5 | HG002compoundhet | het | 95.2389 | 96.5856 | 93.9292 | 78.7201 | 1669 | 59 | 1671 | 108 | 103 | 95.3704 | |
| asubramanian-gatk | INDEL | D16_PLUS | * | het | 97.0125 | 97.6891 | 96.3452 | 79.1579 | 3086 | 73 | 2847 | 108 | 74 | 68.5185 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 81.1540 | 77.3058 | 85.4054 | 60.1508 | 637 | 187 | 632 | 108 | 59 | 54.6296 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.0806 | 99.4197 | 96.7771 | 68.3987 | 3255 | 19 | 3243 | 108 | 105 | 97.2222 | |
| bgallagher-sentieon | SNP | ti | map_l150_m0_e0 | het | 98.4386 | 98.9798 | 97.9033 | 83.1082 | 5045 | 52 | 5043 | 108 | 15 | 13.8889 | |