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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
27701-27750 / 86044 show all | |||||||||||||||
| jlack-gatk | SNP | ti | map_l100_m0_e0 | het | 94.8297 | 98.9201 | 91.0641 | 81.0915 | 13832 | 151 | 13829 | 1357 | 128 | 9.4326 | |
| rpoplin-dv42 | INDEL | I16_PLUS | * | het | 94.8292 | 93.8926 | 95.7847 | 65.3540 | 2552 | 166 | 2545 | 112 | 105 | 93.7500 | |
| ltrigg-rtg2 | INDEL | * | map_l250_m2_e0 | het | 94.8292 | 91.4286 | 98.4925 | 92.1437 | 192 | 18 | 196 | 3 | 0 | 0.0000 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 94.8288 | 92.9433 | 96.7925 | 52.5751 | 3622 | 275 | 4617 | 153 | 140 | 91.5033 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 94.8283 | 92.7831 | 96.9658 | 59.2331 | 2237 | 174 | 2237 | 70 | 66 | 94.2857 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 94.8280 | 94.2961 | 95.3659 | 70.4398 | 777 | 47 | 782 | 38 | 27 | 71.0526 | |
| rpoplin-dv42 | INDEL | D16_PLUS | segdup | * | 94.8276 | 94.8276 | 94.8276 | 93.6819 | 55 | 3 | 55 | 3 | 3 | 100.0000 | |
| astatham-gatk | INDEL | I6_15 | map_l100_m1_e0 | het | 94.8276 | 93.2203 | 96.4912 | 88.7352 | 55 | 4 | 55 | 2 | 1 | 50.0000 | |
| jlack-gatk | SNP | ti | map_siren | hetalt | 94.8276 | 96.4912 | 93.2203 | 77.6515 | 55 | 2 | 55 | 4 | 4 | 100.0000 | |
| dgrover-gatk | INDEL | I1_5 | map_l250_m1_e0 | het | 94.8276 | 91.6667 | 98.2143 | 97.0727 | 55 | 5 | 55 | 1 | 0 | 0.0000 | |
| ltrigg-rtg2 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | hetalt | 94.8276 | 90.1639 | 100.0000 | 55.6452 | 55 | 6 | 55 | 0 | 0 | ||
| anovak-vg | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 94.8271 | 96.9609 | 92.7851 | 60.5360 | 3350 | 105 | 3498 | 272 | 223 | 81.9853 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 94.8267 | 90.2557 | 99.8855 | 32.3046 | 4307 | 465 | 4360 | 5 | 4 | 80.0000 | |
| ltrigg-rtg1 | INDEL | * | map_l250_m2_e0 | * | 94.8253 | 91.2387 | 98.7055 | 93.5812 | 302 | 29 | 305 | 4 | 1 | 25.0000 | |
| ghariani-varprowl | INDEL | D1_5 | map_l150_m2_e1 | homalt | 94.8240 | 92.3387 | 97.4468 | 85.7230 | 229 | 19 | 229 | 6 | 1 | 16.6667 | |
| gduggal-bwaplat | INDEL | * | * | homalt | 94.8233 | 90.5786 | 99.4855 | 59.5744 | 113379 | 11793 | 113311 | 586 | 499 | 85.1536 | |
| ckim-gatk | INDEL | I1_5 | HG002compoundhet | * | 94.8213 | 92.3843 | 97.3904 | 66.1548 | 11415 | 941 | 11420 | 306 | 304 | 99.3464 | |
| hfeng-pmm1 | INDEL | * | map_l100_m2_e1 | hetalt | 94.8207 | 90.1515 | 100.0000 | 87.7654 | 119 | 13 | 121 | 0 | 0 | ||
| astatham-gatk | INDEL | D1_5 | map_l250_m2_e0 | het | 94.8207 | 98.3471 | 91.5385 | 95.9577 | 119 | 2 | 119 | 11 | 1 | 9.0909 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.8204 | 92.5954 | 97.1549 | 61.9830 | 3689 | 295 | 3688 | 108 | 102 | 94.4444 | |
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 94.8193 | 92.4187 | 97.3479 | 49.5090 | 2755 | 226 | 2753 | 75 | 52 | 69.3333 | |
| jpowers-varprowl | INDEL | D1_5 | map_l125_m2_e0 | het | 94.8187 | 95.8115 | 93.8462 | 88.6430 | 732 | 32 | 732 | 48 | 26 | 54.1667 | |
| mlin-fermikit | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.8184 | 94.7230 | 94.9141 | 71.6532 | 1436 | 80 | 1437 | 77 | 43 | 55.8442 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 94.8184 | 97.5347 | 92.2494 | 57.4247 | 633 | 16 | 1095 | 92 | 89 | 96.7391 | |
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 94.8171 | 100.0000 | 90.1449 | 70.2842 | 311 | 0 | 311 | 34 | 33 | 97.0588 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 94.8171 | 94.6358 | 94.9992 | 46.8433 | 11238 | 637 | 11246 | 592 | 535 | 90.3716 | |
| gduggal-snapplat | SNP | tv | map_l100_m1_e0 | * | 94.8170 | 93.1840 | 96.5083 | 77.9815 | 22831 | 1670 | 22830 | 826 | 404 | 48.9104 | |
| jlack-gatk | SNP | ti | map_l150_m0_e0 | * | 94.8167 | 98.1046 | 91.7420 | 86.3569 | 7712 | 149 | 7710 | 694 | 68 | 9.7983 | |
| cchapple-custom | INDEL | D6_15 | map_l125_m2_e0 | het | 94.8166 | 95.7746 | 93.8776 | 89.0503 | 68 | 3 | 92 | 6 | 2 | 33.3333 | |
| cchapple-custom | INDEL | D6_15 | map_l125_m2_e1 | het | 94.8166 | 95.7746 | 93.8776 | 89.3013 | 68 | 3 | 92 | 6 | 2 | 33.3333 | |
| asubramanian-gatk | SNP | * | * | hetalt | 94.8157 | 94.4891 | 95.1445 | 47.6709 | 823 | 48 | 823 | 42 | 2 | 4.7619 | |
| rpoplin-dv42 | INDEL | D6_15 | map_l100_m2_e0 | het | 94.8148 | 97.7099 | 92.0863 | 88.5691 | 128 | 3 | 128 | 11 | 6 | 54.5455 | |
| cchapple-custom | INDEL | D1_5 | map_l250_m1_e0 | * | 94.8142 | 97.0760 | 92.6554 | 94.4234 | 166 | 5 | 164 | 13 | 1 | 7.6923 | |
| hfeng-pmm3 | INDEL | * | HG002compoundhet | * | 94.8142 | 92.3999 | 97.3580 | 58.7757 | 27683 | 2277 | 27564 | 748 | 724 | 96.7914 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.8084 | 91.7464 | 98.0818 | 67.8189 | 767 | 69 | 767 | 15 | 13 | 86.6667 | |
| anovak-vg | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 94.8058 | 95.8213 | 93.8116 | 73.3592 | 2316 | 101 | 2380 | 157 | 134 | 85.3503 | |
| ghariani-varprowl | INDEL | * | map_l100_m2_e0 | homalt | 94.8057 | 91.9112 | 97.8885 | 80.1409 | 1159 | 102 | 1159 | 25 | 8 | 32.0000 | |
| jli-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 94.8052 | 90.1235 | 100.0000 | 75.4209 | 73 | 8 | 73 | 0 | 0 | ||
| rpoplin-dv42 | INDEL | I6_15 | * | hetalt | 94.8036 | 90.5625 | 99.4614 | 37.3252 | 7744 | 807 | 7756 | 42 | 40 | 95.2381 | |
| mlin-fermikit | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 94.8031 | 99.5995 | 90.4474 | 84.6880 | 1492 | 6 | 1496 | 158 | 129 | 81.6456 | |
| hfeng-pmm2 | INDEL | I16_PLUS | HG002compoundhet | * | 94.8024 | 92.3472 | 97.3917 | 52.6892 | 1979 | 164 | 1979 | 53 | 52 | 98.1132 | |
| ckim-dragen | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 94.8012 | 99.6785 | 90.3790 | 71.4642 | 310 | 1 | 310 | 33 | 33 | 100.0000 | |
| ckim-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 94.8006 | 94.5372 | 95.0655 | 64.2896 | 1246 | 72 | 1233 | 64 | 61 | 95.3125 | |
| jli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 94.8006 | 90.6323 | 99.3707 | 28.9674 | 1548 | 160 | 1579 | 10 | 9 | 90.0000 | |
| gduggal-snapfb | SNP | tv | map_l250_m1_e0 | * | 94.8003 | 95.0510 | 94.5509 | 89.8505 | 2516 | 131 | 2516 | 145 | 53 | 36.5517 | |
| jmaeng-gatk | INDEL | * | map_l100_m0_e0 | het | 94.7997 | 98.0411 | 91.7658 | 91.6857 | 1001 | 20 | 1003 | 90 | 4 | 4.4444 | |
| ltrigg-rtg2 | INDEL | D16_PLUS | HG002complexvar | * | 94.7987 | 91.4790 | 98.3685 | 55.6259 | 1503 | 140 | 1447 | 24 | 19 | 79.1667 | |
| gduggal-snapvard | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 94.7982 | 92.4763 | 97.2396 | 66.7223 | 1561 | 127 | 1550 | 44 | 15 | 34.0909 | |
| ckim-dragen | INDEL | I6_15 | segdup | het | 94.7977 | 98.7952 | 91.1111 | 94.6429 | 82 | 1 | 82 | 8 | 0 | 0.0000 | |
| ndellapenna-hhga | INDEL | D6_15 | segdup | het | 94.7959 | 96.7391 | 92.9293 | 94.1351 | 89 | 3 | 92 | 7 | 6 | 85.7143 | |