PrecisionFDA
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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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
74801-74850 / 86044 show all | |||||||||||||||
| ciseli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 85.2750 | 89.1170 | 81.7505 | 62.2628 | 434 | 53 | 439 | 98 | 30 | 30.6122 | |
| ciseli-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 12.6208 | 7.7147 | 34.6667 | 87.4161 | 53 | 634 | 52 | 98 | 77 | 78.5714 | |
| ciseli-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 41.4919 | 29.6496 | 69.0852 | 68.2046 | 220 | 522 | 219 | 98 | 82 | 83.6735 | |
| cchapple-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.2782 | 97.1365 | 99.4471 | 33.4959 | 10109 | 298 | 17626 | 98 | 90 | 91.8367 | |
| ckim-dragen | SNP | * | * | homalt | 99.9725 | 99.9534 | 99.9917 | 17.1093 | 1179611 | 550 | 1179821 | 98 | 80 | 81.6327 | |
| asubramanian-gatk | INDEL | C1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 0.0000 | 0.0000 | 75.5000 | 0 | 0 | 0 | 98 | 0 | 0.0000 | ||
| anovak-vg | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 20.5715 | 13.2114 | 46.4481 | 71.1356 | 65 | 427 | 85 | 98 | 77 | 78.5714 | |
| anovak-vg | INDEL | I16_PLUS | HG002compoundhet | het | 0.0000 | 0.0000 | 45.8564 | 44.3077 | 0 | 47 | 83 | 98 | 29 | 29.5918 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 98.4134 | 99.1518 | 97.6860 | 71.1060 | 3507 | 30 | 4137 | 98 | 96 | 97.9592 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 96.2980 | 98.3871 | 94.2957 | 66.7441 | 1159 | 19 | 1620 | 98 | 95 | 96.9388 | |
| asubramanian-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 93.5466 | 97.8873 | 89.5745 | 84.0136 | 834 | 18 | 842 | 98 | 1 | 1.0204 | |
| anovak-vg | INDEL | I1_5 | map_l125_m0_e0 | homalt | 66.4001 | 91.2281 | 52.1951 | 85.4403 | 104 | 10 | 107 | 98 | 91 | 92.8571 | |
| anovak-vg | SNP | * | lowcmp_SimpleRepeat_quadTR_51to200 | * | 62.2688 | 72.0280 | 54.8387 | 90.2559 | 103 | 40 | 119 | 98 | 35 | 35.7143 | |
| gduggal-snapvard | INDEL | C6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 0.0000 | 0.0000 | 48.1481 | 89.9415 | 0 | 0 | 91 | 98 | 29 | 29.5918 | |
| gduggal-snapfb | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 63.0372 | 53.0172 | 77.7273 | 49.0151 | 246 | 218 | 342 | 98 | 96 | 97.9592 | |
| gduggal-snapfb | SNP | * | func_cds | het | 99.5360 | 99.9462 | 99.1291 | 30.5670 | 11155 | 6 | 11155 | 98 | 1 | 1.0204 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 89.6510 | 84.0909 | 95.9984 | 54.3693 | 4958 | 938 | 2351 | 98 | 96 | 97.9592 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 89.6510 | 84.0909 | 95.9984 | 54.3693 | 4958 | 938 | 2351 | 98 | 96 | 97.9592 | |
| raldana-dualsentieon | SNP | tv | map_l100_m0_e0 | * | 99.1204 | 99.1249 | 99.1158 | 68.4908 | 10987 | 97 | 10986 | 98 | 4 | 4.0816 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 86.8788 | 84.7120 | 89.1593 | 77.2464 | 809 | 146 | 806 | 98 | 98 | 100.0000 | |
| jpowers-varprowl | SNP | tv | map_l250_m0_e0 | het | 89.0728 | 94.0559 | 84.5912 | 95.1175 | 538 | 34 | 538 | 98 | 12 | 12.2449 | |
| jmaeng-gatk | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.1246 | 99.5572 | 98.6958 | 41.6434 | 7419 | 33 | 7416 | 98 | 0 | 0.0000 | |
| jmaeng-gatk | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.7300 | 99.5308 | 97.9420 | 44.2389 | 4667 | 22 | 4664 | 98 | 0 | 0.0000 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.2664 | 99.8896 | 98.6509 | 37.0615 | 7239 | 8 | 7239 | 99 | 98 | 98.9899 | |
| jmaeng-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.7400 | 96.1684 | 99.3638 | 68.4150 | 15461 | 616 | 15462 | 99 | 69 | 69.6970 | |
| jmaeng-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.7400 | 96.1684 | 99.3638 | 68.4150 | 15461 | 616 | 15462 | 99 | 69 | 69.6970 | |
| jli-custom | SNP | ti | map_l100_m0_e0 | * | 99.2096 | 98.8792 | 99.5422 | 63.1044 | 21527 | 244 | 21527 | 99 | 35 | 35.3535 | |
| jmaeng-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.7613 | 94.2669 | 95.2609 | 72.9999 | 2006 | 122 | 1990 | 99 | 89 | 89.8990 | |
| anovak-vg | SNP | * | map_l125_m2_e1 | homalt | 89.7095 | 81.8047 | 99.3055 | 67.9368 | 14342 | 3190 | 14156 | 99 | 83 | 83.8384 | |
| bgallagher-sentieon | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.4660 | 99.4311 | 99.5010 | 59.2336 | 19749 | 113 | 19742 | 99 | 60 | 60.6061 | |
| asubramanian-gatk | INDEL | * | map_l100_m2_e0 | het | 89.6413 | 84.6987 | 95.1965 | 90.0770 | 1954 | 353 | 1962 | 99 | 13 | 13.1313 | |
| asubramanian-gatk | INDEL | C6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 0.0000 | 0.0000 | 75.5556 | 0 | 0 | 0 | 99 | 0 | 0.0000 | ||
| qzeng-custom | INDEL | I1_5 | HG002complexvar | homalt | 99.1245 | 98.9887 | 99.2607 | 46.5706 | 13312 | 136 | 13292 | 99 | 61 | 61.6162 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | het | 86.6705 | 87.5205 | 85.8369 | 72.0400 | 533 | 76 | 600 | 99 | 82 | 82.8283 | |
| ltrigg-rtg2 | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.7692 | 97.9625 | 99.5893 | 34.5018 | 24040 | 500 | 24005 | 99 | 66 | 66.6667 | |
| ltrigg-rtg2 | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.9726 | 98.5812 | 99.3672 | 71.8268 | 15356 | 221 | 15545 | 99 | 39 | 39.3939 | |
| mlin-fermikit | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 88.2477 | 83.3900 | 93.7063 | 86.7826 | 1471 | 293 | 1474 | 99 | 13 | 13.1313 | |
| qzeng-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 95.5593 | 97.6793 | 93.5294 | 90.1841 | 1389 | 33 | 1431 | 99 | 25 | 25.2525 | |
| mlin-fermikit | INDEL | * | map_l150_m1_e0 | homalt | 67.2189 | 61.4719 | 74.1514 | 83.0230 | 284 | 178 | 284 | 99 | 88 | 88.8889 | |
| ndellapenna-hhga | SNP | * | map_l125_m2_e1 | * | 99.1837 | 98.5869 | 99.7877 | 69.5422 | 46535 | 667 | 46535 | 99 | 49 | 49.4949 | |
| hfeng-pmm2 | SNP | tv | map_l125_m0_e0 | * | 98.7817 | 99.0499 | 98.5149 | 77.4668 | 6568 | 63 | 6567 | 99 | 13 | 13.1313 | |
| hfeng-pmm3 | SNP | ti | map_l125_m2_e0 | * | 99.5898 | 99.5076 | 99.6722 | 70.9814 | 30109 | 149 | 30105 | 99 | 16 | 16.1616 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 92.4826 | 97.3404 | 88.0866 | 60.7649 | 732 | 20 | 732 | 99 | 98 | 98.9899 | |
| hfeng-pmm2 | INDEL | D16_PLUS | * | het | 96.8404 | 97.0560 | 96.6258 | 75.3280 | 3066 | 93 | 2835 | 99 | 55 | 55.5556 | |
| hfeng-pmm2 | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 96.5254 | 97.4649 | 95.6039 | 64.9385 | 2153 | 56 | 2153 | 99 | 92 | 92.9293 | |
| egarrison-hhga | SNP | * | map_l100_m2_e1 | het | 99.3694 | 98.9552 | 99.7871 | 65.4429 | 46408 | 490 | 46409 | 99 | 31 | 31.3131 | |
| ckim-vqsr | INDEL | D16_PLUS | * | het | 97.9651 | 99.2719 | 96.6923 | 79.4267 | 3136 | 23 | 2894 | 99 | 69 | 69.6970 | |
| ckim-vqsr | SNP | tv | map_l100_m0_e0 | * | 69.0592 | 53.2118 | 98.3492 | 88.9281 | 5898 | 5186 | 5898 | 99 | 1 | 1.0101 | |
| ckim-vqsr | SNP | tv | map_l100_m0_e0 | het | 79.8556 | 67.3775 | 98.0060 | 89.3473 | 4866 | 2356 | 4866 | 99 | 1 | 1.0101 | |
| ckim-isaac | INDEL | I16_PLUS | HG002complexvar | het | 58.4929 | 47.6692 | 75.6757 | 61.6761 | 317 | 348 | 308 | 99 | 23 | 23.2323 | |