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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
31801-31850 / 86044 show all | |||||||||||||||
| ndellapenna-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.5220 | 99.3296 | 99.7152 | 58.2062 | 3852 | 26 | 3852 | 11 | 4 | 36.3636 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 97.9932 | 99.8407 | 96.2129 | 58.2077 | 3760 | 6 | 3760 | 148 | 145 | 97.9730 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 97.9932 | 99.8407 | 96.2129 | 58.2077 | 3760 | 6 | 3760 | 148 | 145 | 97.9730 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 62.5592 | 92.9577 | 47.1429 | 58.2090 | 66 | 5 | 66 | 74 | 74 | 100.0000 | |
| asubramanian-gatk | INDEL | I1_5 | HG002compoundhet | hetalt | 96.2877 | 93.2540 | 99.5255 | 58.2114 | 10423 | 754 | 10487 | 50 | 46 | 92.0000 | |
| mlin-fermikit | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 98.9023 | 98.7622 | 99.0427 | 58.2117 | 3830 | 48 | 3828 | 37 | 32 | 86.4865 | |
| gduggal-snapplat | SNP | tv | map_siren | homalt | 96.8214 | 93.9095 | 99.9197 | 58.2133 | 16190 | 1050 | 16181 | 13 | 5 | 38.4615 | |
| bgallagher-sentieon | INDEL | I1_5 | * | * | 99.4227 | 99.2586 | 99.5873 | 58.2134 | 149547 | 1117 | 149597 | 620 | 500 | 80.6452 | |
| ckim-vqsr | INDEL | * | HG002complexvar | * | 99.2578 | 98.8640 | 99.6548 | 58.2159 | 76064 | 874 | 75924 | 263 | 222 | 84.4106 | |
| ckim-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | * | 92.5881 | 92.5170 | 92.6593 | 58.2176 | 680 | 55 | 669 | 53 | 51 | 96.2264 | |
| gduggal-snapvard | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 64.0892 | 66.0415 | 62.2490 | 58.2196 | 20741 | 10665 | 29849 | 18102 | 14698 | 81.1954 | |
| gduggal-snapvard | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 64.0892 | 66.0415 | 62.2490 | 58.2196 | 20741 | 10665 | 29849 | 18102 | 14698 | 81.1954 | |
| ckim-isaac | SNP | * | map_l100_m2_e0 | homalt | 73.4369 | 58.0387 | 99.9562 | 58.2196 | 15974 | 11549 | 15974 | 7 | 7 | 100.0000 | |
| jli-custom | INDEL | I1_5 | HG002compoundhet | hetalt | 96.7731 | 93.7729 | 99.9716 | 58.2211 | 10481 | 696 | 10542 | 3 | 3 | 100.0000 | |
| mlin-fermikit | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 86.2115 | 84.1466 | 88.3803 | 58.2216 | 13503 | 2544 | 13516 | 1777 | 1745 | 98.1992 | |
| gduggal-bwavard | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 96.9824 | 96.8153 | 97.1501 | 58.2231 | 27360 | 900 | 27373 | 803 | 642 | 79.9502 | |
| dgrover-gatk | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.8478 | 99.8054 | 99.8902 | 58.2232 | 28205 | 55 | 28208 | 31 | 20 | 64.5161 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_51to200 | * | 96.4824 | 96.0000 | 96.9697 | 58.2278 | 24 | 1 | 32 | 1 | 0 | 0.0000 | |
| gduggal-snapvard | INDEL | D1_5 | HG002compoundhet | * | 63.8171 | 65.9528 | 61.8155 | 58.2289 | 8068 | 4165 | 12360 | 7635 | 5847 | 76.5815 | |
| rpoplin-dv42 | INDEL | D1_5 | * | * | 99.4429 | 99.3110 | 99.5751 | 58.2332 | 145734 | 1011 | 145779 | 622 | 549 | 88.2637 | |
| hfeng-pmm3 | INDEL | D1_5 | HG002complexvar | homalt | 99.8962 | 99.8773 | 99.9151 | 58.2388 | 10585 | 13 | 10590 | 9 | 8 | 88.8889 | |
| raldana-dualsentieon | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.4171 | 99.1580 | 99.6775 | 58.2394 | 2473 | 21 | 2473 | 8 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | I1_5 | HG002complexvar | het | 99.7798 | 99.6646 | 99.8952 | 58.2404 | 18128 | 61 | 18108 | 19 | 9 | 47.3684 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_51to200 | * | 72.2241 | 56.7961 | 99.1597 | 58.2456 | 117 | 89 | 118 | 1 | 0 | 0.0000 | |
| ckim-isaac | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 92.7405 | 88.7846 | 97.0653 | 58.2458 | 8605 | 1087 | 8798 | 266 | 144 | 54.1353 | |
| ltrigg-rtg2 | SNP | ti | map_l125_m2_e0 | het | 98.5679 | 97.3564 | 99.8099 | 58.2477 | 18377 | 499 | 18379 | 35 | 4 | 11.4286 | |
| jmaeng-gatk | SNP | tv | map_siren | homalt | 89.3303 | 80.7367 | 99.9713 | 58.2484 | 13919 | 3321 | 13916 | 4 | 4 | 100.0000 | |
| bgallagher-sentieon | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 94.9615 | 90.9091 | 99.3921 | 58.2487 | 310 | 31 | 327 | 2 | 2 | 100.0000 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | * | 92.6522 | 92.5170 | 92.7878 | 58.2513 | 680 | 55 | 669 | 52 | 50 | 96.1538 | |
| asubramanian-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.1387 | 99.5421 | 98.7386 | 58.2561 | 3913 | 18 | 3914 | 50 | 1 | 2.0000 | |
| mlin-fermikit | SNP | tv | map_l125_m1_e0 | * | 61.8003 | 48.5452 | 85.0126 | 58.2565 | 7775 | 8241 | 7771 | 1370 | 1205 | 87.9562 | |
| cchapple-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 99.8726 | 99.7455 | 100.0000 | 58.2576 | 784 | 2 | 781 | 0 | 0 | ||
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.4861 | 99.5813 | 99.3911 | 58.2577 | 8325 | 35 | 8325 | 51 | 50 | 98.0392 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.4861 | 99.5813 | 99.3911 | 58.2577 | 8325 | 35 | 8325 | 51 | 50 | 98.0392 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 99.7326 | 99.7326 | 99.7326 | 58.2589 | 373 | 1 | 373 | 1 | 0 | 0.0000 | |
| gduggal-snapfb | INDEL | D6_15 | HG002compoundhet | homalt | 3.3072 | 70.8333 | 1.6931 | 58.2597 | 17 | 7 | 16 | 929 | 928 | 99.8924 | |
| asubramanian-gatk | INDEL | * | HG002complexvar | het | 98.7623 | 98.2061 | 99.3248 | 58.2604 | 45383 | 829 | 45014 | 306 | 59 | 19.2810 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 85.2372 | 96.7836 | 76.1521 | 58.2609 | 4303 | 143 | 4825 | 1511 | 1481 | 98.0146 | |
| ckim-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.6319 | 99.8474 | 99.4174 | 58.2620 | 3925 | 6 | 3925 | 23 | 2 | 8.6957 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | * | 90.2544 | 90.2041 | 90.3047 | 58.2659 | 663 | 72 | 652 | 70 | 64 | 91.4286 | |
| hfeng-pmm1 | INDEL | D6_15 | * | het | 98.2571 | 97.6449 | 98.8769 | 58.2726 | 11319 | 273 | 11269 | 128 | 111 | 86.7188 | |
| hfeng-pmm1 | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 77.3333 | 63.0435 | 100.0000 | 58.2734 | 58 | 34 | 58 | 0 | 0 | ||
| jmaeng-gatk | INDEL | * | HG002complexvar | * | 99.2404 | 98.8731 | 99.6104 | 58.2744 | 76071 | 867 | 75939 | 297 | 248 | 83.5017 | |
| ckim-gatk | INDEL | D1_5 | HG002compoundhet | hetalt | 96.5709 | 93.7255 | 99.5943 | 58.2762 | 9575 | 641 | 9575 | 39 | 39 | 100.0000 | |
| gduggal-bwavard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 97.1473 | 97.7063 | 96.5946 | 58.2763 | 3919 | 92 | 3886 | 137 | 15 | 10.9489 | |
| ckim-vqsr | INDEL | D1_5 | HG002compoundhet | hetalt | 96.5656 | 93.7157 | 99.5943 | 58.2787 | 9574 | 642 | 9574 | 39 | 39 | 100.0000 | |
| jmaeng-gatk | INDEL | I1_5 | HG002complexvar | het | 99.6695 | 99.5052 | 99.8344 | 58.2792 | 18099 | 90 | 18081 | 30 | 14 | 46.6667 | |
| hfeng-pmm1 | INDEL | D1_5 | HG002complexvar | homalt | 99.8679 | 99.8207 | 99.9150 | 58.2795 | 10579 | 19 | 10583 | 9 | 8 | 88.8889 | |
| gduggal-snapvard | INDEL | D1_5 | HG002compoundhet | het | 70.6222 | 82.9664 | 61.4755 | 58.2800 | 1432 | 294 | 12099 | 7582 | 5798 | 76.4706 | |
| ckim-vqsr | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.6445 | 99.8219 | 99.4677 | 58.2805 | 3924 | 7 | 3924 | 21 | 2 | 9.5238 | |