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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
13151-13200 / 86044 show all | |||||||||||||||
| ckim-vqsr | SNP | ti | segdup | het | 98.9319 | 98.5619 | 99.3047 | 94.5420 | 11857 | 173 | 11855 | 83 | 4 | 4.8193 | |
| ckim-vqsr | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.3956 | 93.1863 | 99.8338 | 31.7550 | 2366 | 173 | 2403 | 4 | 4 | 100.0000 | |
| ckim-vqsr | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.4006 | 99.5116 | 99.2899 | 63.6333 | 35246 | 173 | 35235 | 252 | 21 | 8.3333 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.1945 | 95.5607 | 98.8851 | 56.8401 | 3724 | 173 | 3725 | 42 | 35 | 83.3333 | |
| ckim-isaac | INDEL | D1_5 | map_l150_m2_e1 | het | 79.5911 | 66.8582 | 98.3146 | 91.5439 | 349 | 173 | 350 | 6 | 2 | 33.3333 | |
| jli-custom | INDEL | D16_PLUS | * | * | 98.0920 | 97.4499 | 98.7427 | 65.2664 | 6611 | 173 | 6597 | 84 | 63 | 75.0000 | |
| jli-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 99.3617 | 99.6215 | 99.1032 | 69.4732 | 45529 | 173 | 45529 | 412 | 31 | 7.5243 | |
| jli-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 99.3617 | 99.6215 | 99.1032 | 69.4732 | 45529 | 173 | 45529 | 412 | 31 | 7.5243 | |
| jli-custom | SNP | tv | map_l100_m2_e0 | * | 99.4221 | 99.3089 | 99.5355 | 64.2177 | 24860 | 173 | 24859 | 116 | 30 | 25.8621 | |
| jli-custom | SNP | tv | map_l100_m2_e1 | * | 99.4258 | 99.3157 | 99.5362 | 64.2630 | 25110 | 173 | 25109 | 117 | 30 | 25.6410 | |
| jmaeng-gatk | INDEL | D16_PLUS | * | * | 97.5405 | 97.4499 | 97.6314 | 70.8962 | 6611 | 173 | 6595 | 160 | 119 | 74.3750 | |
| jmaeng-gatk | INDEL | I16_PLUS | * | hetalt | 95.5588 | 91.7541 | 99.6928 | 55.4720 | 1925 | 173 | 1947 | 6 | 5 | 83.3333 | |
| jmaeng-gatk | INDEL | I16_PLUS | HG002compoundhet | hetalt | 95.6914 | 91.7821 | 99.9485 | 44.7982 | 1921 | 172 | 1941 | 1 | 1 | 100.0000 | |
| jli-custom | SNP | * | HG002complexvar | homalt | 99.9614 | 99.9404 | 99.9823 | 19.9145 | 288402 | 172 | 288385 | 51 | 37 | 72.5490 | |
| jli-custom | SNP | tv | map_l100_m1_e0 | * | 99.4197 | 99.2980 | 99.5417 | 62.1631 | 24329 | 172 | 24328 | 112 | 30 | 26.7857 | |
| hfeng-pmm2 | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.1795 | 96.4441 | 99.9786 | 67.5115 | 4665 | 172 | 4665 | 1 | 0 | 0.0000 | |
| hfeng-pmm3 | SNP | ti | map_l100_m1_e0 | het | 99.5602 | 99.4256 | 99.6952 | 64.3351 | 29770 | 172 | 29763 | 91 | 9 | 9.8901 | |
| gduggal-snapvard | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_51to200 | * | 23.0092 | 16.5049 | 37.9747 | 64.0909 | 34 | 172 | 30 | 49 | 32 | 65.3061 | |
| gduggal-snapplat | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 0.0000 | 0.0000 | 0.0000 | 0 | 172 | 0 | 0 | 0 | |||
| gduggal-snapvard | SNP | tv | map_l150_m0_e0 | * | 87.3397 | 95.8793 | 80.1968 | 85.6633 | 4002 | 172 | 3993 | 986 | 44 | 4.4625 | |
| gduggal-snapvard | SNP | tv | map_l150_m2_e1 | homalt | 97.7665 | 95.8394 | 99.7728 | 73.2888 | 3962 | 172 | 3952 | 9 | 7 | 77.7778 | |
| ghariani-varprowl | SNP | ti | map_l100_m2_e1 | homalt | 99.4248 | 99.0700 | 99.7822 | 63.1662 | 18322 | 172 | 18322 | 40 | 28 | 70.0000 | |
| gduggal-snapfb | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 0.0000 | 0.0000 | 0.0000 | 0 | 172 | 0 | 0 | 0 | |||
| ciseli-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 66.4160 | 55.2083 | 83.3333 | 76.5144 | 212 | 172 | 210 | 42 | 31 | 73.8095 | |
| ckim-gatk | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.1912 | 90.6623 | 98.0059 | 66.8030 | 1670 | 172 | 1671 | 34 | 28 | 82.3529 | |
| ckim-gatk | SNP | ti | HG002compoundhet | * | 99.4312 | 99.0159 | 99.8500 | 36.2044 | 17306 | 172 | 17306 | 26 | 21 | 80.7692 | |
| qzeng-custom | INDEL | I1_5 | map_l125_m2_e1 | het | 78.2603 | 66.1417 | 95.8159 | 93.1509 | 336 | 172 | 458 | 20 | 9 | 45.0000 | |
| bgallagher-sentieon | SNP | ti | map_l125_m2_e0 | * | 99.3281 | 99.4316 | 99.2249 | 72.6504 | 30086 | 172 | 30082 | 235 | 42 | 17.8723 | |
| bgallagher-sentieon | SNP | ti | map_l125_m2_e1 | * | 99.3333 | 99.4373 | 99.2295 | 72.6907 | 30397 | 172 | 30393 | 236 | 42 | 17.7966 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 90.8242 | 84.7922 | 97.7800 | 34.6306 | 959 | 172 | 969 | 22 | 17 | 77.2727 | |
| raldana-dualsentieon | SNP | ti | map_l100_m0_e0 | het | 98.6534 | 98.7699 | 98.5371 | 69.8191 | 13811 | 172 | 13808 | 205 | 2 | 0.9756 | |
| raldana-dualsentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 95.8304 | 94.6417 | 97.0494 | 60.1686 | 3038 | 172 | 3026 | 92 | 90 | 97.8261 | |
| rpoplin-dv42 | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 89.1786 | 80.8250 | 99.4580 | 43.1871 | 725 | 172 | 734 | 4 | 4 | 100.0000 | |
| rpoplin-dv42 | SNP | * | map_l125_m0_e0 | het | 98.6495 | 98.6418 | 98.6571 | 74.4583 | 12492 | 172 | 12489 | 170 | 97 | 57.0588 | |
| rpoplin-dv42 | SNP | * | map_siren | homalt | 99.7831 | 99.6882 | 99.8783 | 53.6066 | 54984 | 172 | 54983 | 67 | 63 | 94.0299 | |
| gduggal-bwavard | SNP | tv | map_l125_m2_e1 | het | 93.2098 | 98.3701 | 88.5639 | 83.4663 | 10381 | 172 | 10354 | 1337 | 65 | 4.8616 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.5573 | 99.3217 | 99.7940 | 54.6839 | 25187 | 172 | 25185 | 52 | 39 | 75.0000 | |
| gduggal-bwaplat | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 71.8766 | 64.7541 | 80.7595 | 87.1336 | 316 | 172 | 319 | 76 | 1 | 1.3158 | |
| eyeh-varpipe | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 62.4607 | 73.6600 | 54.2174 | 39.2369 | 481 | 172 | 2314 | 1954 | 1945 | 99.5394 | |
| eyeh-varpipe | INDEL | D6_15 | HG002compoundhet | het | 60.1947 | 80.0234 | 48.2412 | 75.0000 | 685 | 171 | 96 | 103 | 100 | 97.0874 | |
| gduggal-bwavard | SNP | tv | map_l125_m2_e0 | het | 93.1678 | 98.3624 | 88.4944 | 83.4152 | 10271 | 171 | 10245 | 1332 | 64 | 4.8048 | |
| gduggal-bwavard | INDEL | D1_5 | map_siren | * | 93.7516 | 95.1544 | 92.3895 | 83.9860 | 3358 | 171 | 3302 | 272 | 95 | 34.9265 | |
| gduggal-bwaplat | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 70.3704 | 55.0000 | 97.6636 | 65.3160 | 209 | 171 | 209 | 5 | 5 | 100.0000 | |
| gduggal-bwaplat | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 90.1566 | 82.3347 | 99.6207 | 65.0618 | 797 | 171 | 788 | 3 | 3 | 100.0000 | |
| gduggal-bwaplat | INDEL | I6_15 | HG002complexvar | homalt | 91.5364 | 85.9143 | 97.9458 | 60.0075 | 1043 | 171 | 1049 | 22 | 17 | 77.2727 | |
| gduggal-bwaplat | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 73.8416 | 59.0909 | 98.4064 | 66.3539 | 247 | 171 | 247 | 4 | 0 | 0.0000 | |
| eyeh-varpipe | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.8170 | 99.3884 | 96.2946 | 56.5927 | 27788 | 171 | 27079 | 1042 | 134 | 12.8599 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 75.8133 | 61.0478 | 100.0000 | 40.6250 | 268 | 171 | 19 | 0 | 0 | ||
| gduggal-bwafb | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 52.0278 | 40.2098 | 73.6842 | 72.8571 | 115 | 171 | 14 | 5 | 5 | 100.0000 | |
| gduggal-bwafb | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 54.0397 | 38.7097 | 89.4737 | 72.4638 | 108 | 171 | 34 | 4 | 4 | 100.0000 | |