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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
1351-1400 / 86044 show all | |||||||||||||||
| gduggal-bwavard | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 40.2625 | 37.4075 | 43.5894 | 47.0109 | 3538 | 5920 | 3512 | 4545 | 4494 | 98.8779 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 85.0825 | 75.8761 | 96.8314 | 49.6990 | 18620 | 5920 | 18611 | 609 | 395 | 64.8604 | |
| qzeng-custom | INDEL | * | * | hetalt | 86.3714 | 76.5503 | 99.0835 | 60.3958 | 19319 | 5918 | 5730 | 53 | 41 | 77.3585 | |
| gduggal-snapplat | INDEL | D1_5 | * | hetalt | 56.5026 | 42.2548 | 85.2469 | 84.6995 | 4329 | 5916 | 4403 | 762 | 572 | 75.0656 | |
| jmaeng-gatk | SNP | ti | * | homalt | 99.6264 | 99.2642 | 99.9912 | 16.0789 | 797129 | 5909 | 797120 | 70 | 46 | 65.7143 | |
| qzeng-custom | INDEL | * | HG002compoundhet | hetalt | 86.4434 | 76.5369 | 99.2955 | 48.8192 | 19272 | 5908 | 5638 | 40 | 29 | 72.5000 | |
| gduggal-bwavard | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 0.0000 | 0.5221 | 0.0000 | 0.0000 | 31 | 5907 | 0 | 0 | 0 | ||
| anovak-vg | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 0.0000 | 27.7254 | 0.0000 | 0.0000 | 2266 | 5907 | 0 | 0 | 0 | ||
| eyeh-varpipe | INDEL | * | HG002complexvar | * | 93.6611 | 92.3263 | 95.0350 | 54.2841 | 71034 | 5904 | 71760 | 3749 | 3600 | 96.0256 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 52.9384 | 36.4654 | 96.5577 | 59.1585 | 3388 | 5903 | 3899 | 139 | 129 | 92.8058 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 52.9384 | 36.4654 | 96.5577 | 59.1585 | 3388 | 5903 | 3899 | 139 | 129 | 92.8058 | |
| gduggal-snapplat | INDEL | D1_5 | HG002compoundhet | hetalt | 57.5062 | 42.2964 | 89.7972 | 79.0515 | 4321 | 5895 | 4383 | 498 | 424 | 85.1406 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 0.0000 | 0.7747 | 0.0000 | 0.0000 | 46 | 5892 | 0 | 0 | 0 | ||
| gduggal-bwafb | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 95.5779 | 93.7628 | 97.4647 | 70.7003 | 88558 | 5891 | 94531 | 2459 | 2226 | 90.5246 | |
| ndellapenna-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 78.1075 | 64.7471 | 98.4152 | 46.2255 | 10816 | 5889 | 10060 | 162 | 132 | 81.4815 | |
| ndellapenna-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 78.1075 | 64.7471 | 98.4152 | 46.2255 | 10816 | 5889 | 10060 | 162 | 132 | 81.4815 | |
| ghariani-varprowl | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 0.0000 | 0.9431 | 0.0000 | 0.0000 | 56 | 5882 | 0 | 0 | 0 | ||
| gduggal-bwavard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 0.0000 | 0.4579 | 0.0000 | 0.0000 | 27 | 5869 | 0 | 0 | 0 | ||
| gduggal-bwavard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 0.0000 | 0.4579 | 0.0000 | 0.0000 | 27 | 5869 | 0 | 0 | 0 | ||
| jpowers-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 0.0000 | 0.5767 | 0.0000 | 0.0000 | 34 | 5862 | 0 | 0 | 0 | ||
| jpowers-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 0.0000 | 0.5767 | 0.0000 | 0.0000 | 34 | 5862 | 0 | 0 | 0 | ||
| anovak-vg | SNP | * | map_l125_m1_e0 | * | 81.0489 | 87.0673 | 75.8087 | 74.5245 | 39465 | 5862 | 39018 | 12451 | 2766 | 22.2151 | |
| asubramanian-gatk | SNP | ti | map_l150_m1_e0 | homalt | 33.4015 | 20.0491 | 100.0000 | 91.6220 | 1469 | 5858 | 1469 | 0 | 0 | ||
| ghariani-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 0.0000 | 0.6615 | 0.0000 | 0.0000 | 39 | 5857 | 0 | 0 | 0 | ||
| ghariani-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 0.0000 | 0.6615 | 0.0000 | 0.0000 | 39 | 5857 | 0 | 0 | 0 | ||
| anovak-vg | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 0.0000 | 27.6590 | 0.0000 | 0.0000 | 2239 | 5856 | 0 | 0 | 0 | ||
| ckim-gatk | SNP | * | map_siren | het | 95.8468 | 93.5653 | 98.2423 | 71.0090 | 85136 | 5855 | 85122 | 1523 | 109 | 7.1569 | |
| qzeng-custom | SNP | * | map_l100_m2_e1 | homalt | 87.9899 | 78.9574 | 99.3560 | 60.6459 | 21947 | 5849 | 21600 | 140 | 134 | 95.7143 | |
| ckim-vqsr | SNP | ti | map_l125_m2_e1 | het | 81.5245 | 69.3666 | 98.8501 | 88.6777 | 13240 | 5847 | 13238 | 154 | 3 | 1.9481 | |
| eyeh-varpipe | INDEL | D6_15 | HG002compoundhet | * | 39.7758 | 35.3560 | 45.4585 | 32.6471 | 3193 | 5838 | 3138 | 3765 | 3754 | 99.7078 | |
| qzeng-custom | SNP | * | map_l100_m2_e0 | homalt | 87.8998 | 78.8141 | 99.3533 | 60.6693 | 21692 | 5831 | 21356 | 139 | 133 | 95.6835 | |
| ghariani-varprowl | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 43.5285 | 42.1324 | 45.0202 | 75.7921 | 4244 | 5829 | 4231 | 5167 | 5021 | 97.1744 | |
| qzeng-custom | SNP | * | map_l150_m2_e1 | het | 81.7356 | 71.3795 | 95.6069 | 89.7988 | 14535 | 5828 | 14407 | 662 | 554 | 83.6858 | |
| ckim-gatk | SNP | tv | * | * | 99.5705 | 99.3991 | 99.7425 | 27.2376 | 963863 | 5827 | 963776 | 2488 | 84 | 3.3762 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 76.0331 | 67.0590 | 87.7802 | 43.4475 | 11850 | 5821 | 12686 | 1766 | 1744 | 98.7542 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 76.0331 | 67.0590 | 87.7802 | 43.4475 | 11850 | 5821 | 12686 | 1766 | 1744 | 98.7542 | |
| qzeng-custom | SNP | * | map_l100_m1_e0 | homalt | 87.6866 | 78.4579 | 99.3758 | 57.2534 | 21186 | 5817 | 20855 | 131 | 129 | 98.4733 | |
| gduggal-bwavard | SNP | ti | HG002complexvar | homalt | 98.4467 | 96.9948 | 99.9428 | 17.4866 | 187650 | 5814 | 183526 | 105 | 78 | 74.2857 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 62.8790 | 57.8527 | 68.8617 | 41.8554 | 7975 | 5810 | 7937 | 3589 | 3504 | 97.6317 | |
| ckim-vqsr | SNP | ti | map_l125_m2_e0 | het | 81.4281 | 69.2308 | 98.8426 | 88.6749 | 13068 | 5808 | 13066 | 153 | 3 | 1.9608 | |
| mlin-fermikit | SNP | tv | map_l125_m2_e1 | het | 61.6520 | 44.9730 | 97.9955 | 67.0300 | 4746 | 5807 | 4742 | 97 | 1 | 1.0309 | |
| gduggal-bwaplat | SNP | ti | HG002complexvar | homalt | 98.4485 | 97.0077 | 99.9328 | 19.1570 | 187674 | 5789 | 187425 | 126 | 109 | 86.5079 | |
| qzeng-custom | SNP | * | map_l150_m2_e0 | het | 81.6474 | 71.2611 | 95.5780 | 89.7912 | 14347 | 5786 | 14222 | 658 | 550 | 83.5866 | |
| mlin-fermikit | SNP | tv | map_l125_m2_e0 | het | 61.4279 | 44.7328 | 98.0050 | 66.8730 | 4671 | 5771 | 4667 | 95 | 1 | 1.0526 | |
| ckim-vqsr | SNP | tv | map_l150_m2_e1 | * | 66.1510 | 49.8261 | 98.3860 | 92.1390 | 5731 | 5771 | 5730 | 94 | 0 | 0.0000 | |
| gduggal-snapvard | SNP | tv | * | het | 98.6977 | 99.0250 | 98.3726 | 31.6253 | 585935 | 5769 | 583366 | 9651 | 1423 | 14.7446 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 83.8931 | 74.1034 | 96.6631 | 64.8282 | 16488 | 5762 | 16483 | 569 | 336 | 59.0510 | |
| mlin-fermikit | SNP | ti | map_l100_m2_e1 | homalt | 75.6197 | 68.8710 | 83.8347 | 52.0014 | 12737 | 5757 | 12737 | 2456 | 2363 | 96.2134 | |
| qzeng-custom | SNP | * | map_l100_m0_e0 | het | 82.7631 | 72.8602 | 95.7815 | 86.9859 | 15450 | 5755 | 15326 | 675 | 562 | 83.2593 | |
| ndellapenna-hhga | SNP | * | * | * | 99.8818 | 99.8118 | 99.9519 | 18.1821 | 3048871 | 5748 | 3048919 | 1468 | 467 | 31.8120 | |