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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
35001-35050 / 86044 show all | |||||||||||||||
| gduggal-snapvard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 88.7849 | 97.2272 | 81.6917 | 72.6965 | 3822 | 109 | 3757 | 842 | 12 | 1.4252 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 88.7848 | 98.4043 | 80.8786 | 56.7114 | 185 | 3 | 313 | 74 | 73 | 98.6486 | |
| cchapple-custom | INDEL | I6_15 | map_l100_m0_e0 | * | 88.7845 | 84.8485 | 93.1034 | 92.0330 | 28 | 5 | 27 | 2 | 1 | 50.0000 | |
| gduggal-snapvard | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 88.7830 | 97.7024 | 81.3559 | 76.1187 | 893 | 21 | 864 | 198 | 3 | 1.5152 | |
| gduggal-snapfb | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | het | 88.7788 | 99.0616 | 80.4299 | 50.4389 | 4645 | 44 | 4677 | 1138 | 26 | 2.2847 | |
| gduggal-bwaplat | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 88.7695 | 83.2661 | 95.0518 | 86.1448 | 826 | 166 | 826 | 43 | 4 | 9.3023 | |
| mlin-fermikit | INDEL | D16_PLUS | HG002complexvar | * | 88.7656 | 86.9142 | 90.6977 | 68.5511 | 1428 | 215 | 1443 | 148 | 132 | 89.1892 | |
| ckim-isaac | SNP | ti | HG002compoundhet | * | 88.7627 | 82.1776 | 96.4952 | 32.6037 | 14363 | 3115 | 14647 | 532 | 421 | 79.1353 | |
| gduggal-snapplat | SNP | ti | map_l250_m2_e0 | homalt | 88.7618 | 79.9314 | 99.7857 | 88.9135 | 1398 | 351 | 1397 | 3 | 3 | 100.0000 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 88.7617 | 87.5000 | 90.0602 | 60.8952 | 252 | 36 | 598 | 66 | 60 | 90.9091 | |
| ckim-isaac | INDEL | I6_15 | * | het | 88.7567 | 85.9065 | 91.8024 | 48.2080 | 8619 | 1414 | 8623 | 770 | 554 | 71.9481 | |
| gduggal-snapplat | SNP | ti | map_l250_m2_e1 | * | 88.7551 | 83.8849 | 94.2257 | 93.7237 | 4258 | 818 | 4259 | 261 | 138 | 52.8736 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 88.7546 | 84.9330 | 92.9364 | 52.1776 | 1522 | 270 | 1592 | 121 | 119 | 98.3471 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 88.7545 | 83.2610 | 95.0242 | 30.5643 | 1343 | 270 | 6092 | 319 | 295 | 92.4765 | |
| rpoplin-dv42 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 88.7503 | 87.5000 | 90.0369 | 78.1275 | 252 | 36 | 244 | 27 | 25 | 92.5926 | |
| ghariani-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 88.7492 | 96.2428 | 82.3383 | 73.2890 | 333 | 13 | 331 | 71 | 64 | 90.1408 | |
| ckim-gatk | INDEL | D16_PLUS | map_l100_m2_e1 | het | 88.7476 | 96.0784 | 82.4561 | 96.6569 | 49 | 2 | 47 | 10 | 4 | 40.0000 | |
| hfeng-pmm2 | INDEL | D16_PLUS | map_l100_m2_e1 | het | 88.7476 | 96.0784 | 82.4561 | 95.1199 | 49 | 2 | 47 | 10 | 3 | 30.0000 | |
| ghariani-varprowl | SNP | tv | map_l250_m0_e0 | het | 88.7470 | 97.2028 | 81.6446 | 94.8874 | 556 | 16 | 556 | 125 | 12 | 9.6000 | |
| gduggal-snapvard | INDEL | I1_5 | map_l100_m0_e0 | het | 88.7467 | 97.8528 | 81.1912 | 89.9796 | 319 | 7 | 518 | 120 | 44 | 36.6667 | |
| anovak-vg | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 88.7453 | 86.9963 | 90.5660 | 76.6520 | 475 | 71 | 480 | 50 | 32 | 64.0000 | |
| gduggal-snapplat | SNP | ti | map_l250_m2_e0 | het | 88.7434 | 85.9865 | 91.6830 | 94.7245 | 2798 | 456 | 2800 | 254 | 132 | 51.9685 | |
| gduggal-snapplat | SNP | ti | map_l250_m2_e0 | * | 88.7392 | 83.8658 | 94.2139 | 93.6830 | 4200 | 808 | 4201 | 258 | 136 | 52.7132 | |
| jpowers-varprowl | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 88.7392 | 94.6612 | 83.5145 | 64.2718 | 461 | 26 | 461 | 91 | 89 | 97.8022 | |
| gduggal-snapplat | SNP | ti | map_l250_m2_e1 | het | 88.7384 | 85.9654 | 91.6963 | 94.7638 | 2836 | 463 | 2838 | 257 | 134 | 52.1401 | |
| gduggal-bwaplat | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 88.7324 | 79.7468 | 100.0000 | 33.2155 | 189 | 48 | 189 | 0 | 0 | ||
| ciseli-custom | SNP | ti | map_l125_m2_e1 | homalt | 88.7321 | 87.6244 | 89.8682 | 67.8893 | 10040 | 1418 | 10023 | 1130 | 915 | 80.9735 | |
| astatham-gatk | SNP | * | map_l100_m0_e0 | het | 88.7308 | 80.0000 | 99.6007 | 77.5238 | 16964 | 4241 | 16960 | 68 | 23 | 33.8235 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 88.7305 | 90.6250 | 86.9136 | 84.8258 | 348 | 36 | 352 | 53 | 21 | 39.6226 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 88.7284 | 98.2608 | 80.8820 | 41.3226 | 10226 | 181 | 10564 | 2497 | 2416 | 96.7561 | |
| ghariani-varprowl | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 88.7251 | 97.6459 | 81.2979 | 79.6603 | 2945 | 71 | 2969 | 683 | 7 | 1.0249 | |
| cchapple-custom | INDEL | D16_PLUS | map_l150_m2_e0 | het | 88.7246 | 93.7500 | 84.2105 | 94.4928 | 15 | 1 | 16 | 3 | 0 | 0.0000 | |
| cchapple-custom | INDEL | D16_PLUS | map_l150_m2_e1 | het | 88.7246 | 93.7500 | 84.2105 | 94.6023 | 15 | 1 | 16 | 3 | 0 | 0.0000 | |
| ltrigg-rtg2 | INDEL | D16_PLUS | map_l100_m0_e0 | het | 88.7246 | 84.2105 | 93.7500 | 87.4016 | 16 | 3 | 15 | 1 | 0 | 0.0000 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 88.7211 | 90.1328 | 87.3529 | 74.4841 | 475 | 52 | 594 | 86 | 81 | 94.1860 | |
| gduggal-snapvard | SNP | tv | map_l150_m2_e1 | het | 88.7208 | 97.3054 | 81.5281 | 85.1064 | 7150 | 198 | 7128 | 1615 | 97 | 6.0062 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 88.7180 | 93.5323 | 84.3750 | 85.4922 | 188 | 13 | 189 | 35 | 17 | 48.5714 | |
| jli-custom | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 88.7128 | 96.9359 | 81.7757 | 44.7028 | 348 | 11 | 350 | 78 | 77 | 98.7179 | |
| ndellapenna-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 88.7114 | 85.5263 | 92.1429 | 90.3448 | 130 | 22 | 129 | 11 | 4 | 36.3636 | |
| rpoplin-dv42 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 88.7097 | 80.8824 | 98.2143 | 96.7098 | 55 | 13 | 55 | 1 | 1 | 100.0000 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | hetalt | 88.7097 | 79.7101 | 100.0000 | 53.3898 | 55 | 14 | 55 | 0 | 0 | ||
| gduggal-snapplat | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 88.7092 | 85.8663 | 91.7468 | 78.0293 | 15328 | 2523 | 15363 | 1382 | 108 | 7.8148 | |
| qzeng-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 88.7085 | 94.0415 | 83.9479 | 92.5405 | 363 | 23 | 387 | 74 | 11 | 14.8649 | |
| anovak-vg | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 88.7047 | 91.7202 | 85.8812 | 83.6926 | 2426 | 219 | 2573 | 423 | 179 | 42.3168 | |
| jmaeng-gatk | INDEL | D16_PLUS | map_l100_m1_e0 | het | 88.7014 | 95.6522 | 82.6923 | 96.1223 | 44 | 2 | 43 | 9 | 4 | 44.4444 | |
| hfeng-pmm2 | INDEL | D16_PLUS | map_l100_m1_e0 | het | 88.7014 | 95.6522 | 82.6923 | 94.6776 | 44 | 2 | 43 | 9 | 3 | 33.3333 | |
| ckim-vqsr | INDEL | D16_PLUS | map_l100_m1_e0 | het | 88.7014 | 95.6522 | 82.6923 | 96.3989 | 44 | 2 | 43 | 9 | 4 | 44.4444 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 88.7013 | 84.8315 | 92.9412 | 72.5806 | 151 | 27 | 158 | 12 | 4 | 33.3333 | |
| gduggal-bwafb | INDEL | D6_15 | HG002compoundhet | * | 88.7012 | 84.9518 | 92.7969 | 32.0774 | 7672 | 1359 | 8799 | 683 | 663 | 97.0717 | |
| ckim-gatk | SNP | ti | map_l125_m1_e0 | het | 88.7011 | 81.4464 | 97.3746 | 85.8996 | 14877 | 3389 | 14873 | 401 | 40 | 9.9751 | |