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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
29251-29300 / 86044 show all | |||||||||||||||
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 93.9895 | 89.5064 | 98.9454 | 55.5533 | 2158 | 253 | 2158 | 23 | 21 | 91.3043 | |
| ckim-gatk | INDEL | * | HG002compoundhet | * | 93.9895 | 92.8338 | 95.1743 | 62.6651 | 27813 | 2147 | 27690 | 1404 | 1391 | 99.0741 | |
| gduggal-snapplat | SNP | * | map_l125_m2_e0 | * | 93.9886 | 91.9975 | 96.0678 | 81.8481 | 42984 | 3739 | 42999 | 1760 | 941 | 53.4659 | |
| gduggal-bwavard | INDEL | D1_5 | segdup | het | 93.9882 | 98.5549 | 89.8260 | 96.1006 | 682 | 10 | 671 | 76 | 57 | 75.0000 | |
| asubramanian-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 93.9874 | 90.0901 | 98.2372 | 88.6401 | 600 | 66 | 613 | 11 | 6 | 54.5455 | |
| asubramanian-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 93.9874 | 90.0901 | 98.2372 | 88.6401 | 600 | 66 | 613 | 11 | 6 | 54.5455 | |
| hfeng-pmm2 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 93.9873 | 91.5781 | 96.5267 | 61.0569 | 1207 | 111 | 1195 | 43 | 42 | 97.6744 | |
| jlack-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 93.9867 | 89.1496 | 99.3789 | 58.6118 | 304 | 37 | 320 | 2 | 1 | 50.0000 | |
| rpoplin-dv42 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 93.9862 | 93.5323 | 94.4444 | 85.3550 | 188 | 13 | 187 | 11 | 5 | 45.4545 | |
| gduggal-snapplat | SNP | ti | map_l125_m1_e0 | het | 93.9862 | 93.7479 | 94.2256 | 83.3757 | 17124 | 1142 | 17150 | 1051 | 571 | 54.3292 | |
| eyeh-varpipe | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 93.9854 | 96.3753 | 91.7112 | 76.9278 | 452 | 17 | 343 | 31 | 12 | 38.7097 | |
| gduggal-bwavard | INDEL | I1_5 | map_l150_m2_e0 | * | 93.9848 | 95.5684 | 92.4528 | 91.6272 | 496 | 23 | 490 | 40 | 14 | 35.0000 | |
| eyeh-varpipe | INDEL | * | HG002complexvar | homalt | 93.9842 | 95.4231 | 92.5880 | 51.8445 | 25790 | 1237 | 26070 | 2087 | 2039 | 97.7000 | |
| ndellapenna-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 93.9839 | 95.1498 | 92.8462 | 56.1753 | 10927 | 557 | 10928 | 842 | 429 | 50.9501 | |
| gduggal-bwavard | INDEL | I1_5 | map_l100_m1_e0 | * | 93.9837 | 93.8013 | 94.1667 | 85.5706 | 1256 | 83 | 1243 | 77 | 36 | 46.7532 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 93.9836 | 91.7841 | 96.2911 | 69.5456 | 3452 | 309 | 3453 | 133 | 125 | 93.9850 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 93.9836 | 91.7841 | 96.2911 | 69.5456 | 3452 | 309 | 3453 | 133 | 125 | 93.9850 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 93.9827 | 89.0533 | 99.4898 | 29.9773 | 2107 | 259 | 2145 | 11 | 11 | 100.0000 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 93.9827 | 89.0533 | 99.4898 | 29.9773 | 2107 | 259 | 2145 | 11 | 11 | 100.0000 | |
| gduggal-bwavard | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 93.9826 | 95.8648 | 92.1728 | 78.1956 | 4567 | 197 | 4522 | 384 | 48 | 12.5000 | |
| rpoplin-dv42 | INDEL | D16_PLUS | HG002complexvar | * | 93.9813 | 92.4528 | 95.5612 | 63.5376 | 1519 | 124 | 1507 | 70 | 64 | 91.4286 | |
| jmaeng-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 93.9805 | 88.9241 | 99.6466 | 70.0529 | 281 | 35 | 282 | 1 | 1 | 100.0000 | |
| ckim-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 93.9805 | 88.9241 | 99.6466 | 70.1162 | 281 | 35 | 282 | 1 | 1 | 100.0000 | |
| astatham-gatk | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 93.9775 | 89.0167 | 99.5238 | 40.0705 | 3404 | 420 | 3553 | 17 | 17 | 100.0000 | |
| asubramanian-gatk | INDEL | I6_15 | func_cds | * | 93.9759 | 90.6977 | 97.5000 | 42.8571 | 39 | 4 | 39 | 1 | 1 | 100.0000 | |
| jlack-gatk | SNP | * | map_l100_m1_e0 | hetalt | 93.9759 | 95.1220 | 92.8571 | 84.6154 | 39 | 2 | 39 | 3 | 3 | 100.0000 | |
| jlack-gatk | SNP | tv | map_l100_m1_e0 | hetalt | 93.9759 | 95.1220 | 92.8571 | 84.6154 | 39 | 2 | 39 | 3 | 3 | 100.0000 | |
| hfeng-pmm2 | INDEL | * | map_l100_m2_e1 | hetalt | 93.9759 | 88.6364 | 100.0000 | 88.0522 | 117 | 15 | 119 | 0 | 0 | ||
| ltrigg-rtg2 | INDEL | I1_5 | map_l100_m1_e0 | hetalt | 93.9759 | 88.6364 | 100.0000 | 93.3227 | 39 | 5 | 42 | 0 | 0 | ||
| ltrigg-rtg2 | INDEL | I1_5 | map_l100_m2_e0 | hetalt | 93.9759 | 88.6364 | 100.0000 | 93.8053 | 39 | 5 | 42 | 0 | 0 | ||
| jmaeng-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_gt10 | het | 93.9759 | 88.6364 | 100.0000 | 97.0787 | 39 | 5 | 39 | 0 | 0 | ||
| gduggal-snapfb | SNP | * | map_l100_m1_e0 | hetalt | 93.9759 | 95.1220 | 92.8571 | 85.7627 | 39 | 2 | 39 | 3 | 0 | 0.0000 | |
| gduggal-snapfb | SNP | tv | map_l100_m1_e0 | hetalt | 93.9759 | 95.1220 | 92.8571 | 85.7627 | 39 | 2 | 39 | 3 | 0 | 0.0000 | |
| qzeng-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 93.9750 | 94.3820 | 93.5714 | 66.5072 | 84 | 5 | 131 | 9 | 2 | 22.2222 | |
| rpoplin-dv42 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 93.9710 | 90.6042 | 97.5975 | 61.3424 | 5728 | 594 | 5728 | 141 | 133 | 94.3262 | |
| rpoplin-dv42 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 93.9710 | 90.6042 | 97.5975 | 61.3424 | 5728 | 594 | 5728 | 141 | 133 | 94.3262 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 93.9702 | 92.4431 | 95.5486 | 30.3243 | 1260 | 103 | 11269 | 525 | 504 | 96.0000 | |
| jlack-gatk | SNP | * | map_l150_m0_e0 | * | 93.9698 | 98.0635 | 90.2042 | 86.8496 | 11799 | 233 | 11796 | 1281 | 106 | 8.2748 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 93.9690 | 91.1857 | 96.9275 | 72.3266 | 14204 | 1373 | 12524 | 397 | 332 | 83.6272 | |
| gduggal-bwavard | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 93.9684 | 95.8443 | 92.1644 | 78.1320 | 1453 | 63 | 1435 | 122 | 17 | 13.9344 | |
| astatham-gatk | INDEL | I1_5 | map_l125_m1_e0 | het | 93.9683 | 89.7119 | 98.6486 | 88.3311 | 436 | 50 | 438 | 6 | 0 | 0.0000 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 93.9659 | 93.6956 | 94.2379 | 71.6964 | 60369 | 4062 | 60447 | 3696 | 3375 | 91.3149 | |
| ckim-gatk | INDEL | I1_5 | map_l250_m2_e0 | * | 93.9655 | 96.4602 | 91.5966 | 97.4551 | 109 | 4 | 109 | 10 | 2 | 20.0000 | |
| gduggal-snapfb | SNP | tv | map_l250_m0_e0 | * | 93.9650 | 94.6405 | 93.2990 | 94.3329 | 724 | 41 | 724 | 52 | 12 | 23.0769 | |
| gduggal-bwavard | INDEL | I1_5 | map_l100_m2_e0 | * | 93.9648 | 93.7865 | 94.1438 | 86.6818 | 1283 | 85 | 1270 | 79 | 38 | 48.1013 | |
| ckim-vqsr | INDEL | * | HG002compoundhet | * | 93.9622 | 92.7503 | 95.2061 | 62.6940 | 27788 | 2172 | 27665 | 1393 | 1381 | 99.1385 | |
| cchapple-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 93.9600 | 91.6530 | 96.3860 | 42.0652 | 560 | 51 | 2347 | 88 | 80 | 90.9091 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | hetalt | 93.9597 | 93.3333 | 94.5946 | 89.0208 | 56 | 4 | 35 | 2 | 2 | 100.0000 | |
| jpowers-varprowl | INDEL | D1_5 | map_l150_m2_e0 | het | 93.9597 | 95.3307 | 92.6276 | 90.5316 | 490 | 24 | 490 | 39 | 20 | 51.2821 | |
| jpowers-varprowl | SNP | tv | tech_badpromoters | * | 93.9597 | 97.2222 | 90.9091 | 63.5071 | 70 | 2 | 70 | 7 | 1 | 14.2857 | |