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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
46301-46350 / 86044 show all | |||||||||||||||
| hfeng-pmm3 | INDEL | I16_PLUS | HG002complexvar | hetalt | 96.8227 | 94.6269 | 99.1228 | 69.7613 | 317 | 18 | 339 | 3 | 3 | 100.0000 | |
| hfeng-pmm2 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 96.2500 | 99.0354 | 93.6170 | 69.7610 | 308 | 3 | 308 | 21 | 20 | 95.2381 | |
| jpowers-varprowl | SNP | tv | map_l100_m0_e0 | homalt | 98.7169 | 98.0239 | 99.4198 | 69.7608 | 3770 | 76 | 3770 | 22 | 12 | 54.5455 | |
| cchapple-custom | SNP | tv | map_l100_m1_e0 | * | 97.1628 | 97.8613 | 96.4743 | 69.7586 | 23977 | 524 | 23970 | 876 | 133 | 15.1826 | |
| ckim-dragen | INDEL | D6_15 | map_l100_m1_e0 | hetalt | 95.3846 | 91.1765 | 100.0000 | 69.7561 | 62 | 6 | 62 | 0 | 0 | ||
| jli-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 94.1575 | 89.2405 | 99.6479 | 69.7551 | 282 | 34 | 283 | 1 | 1 | 100.0000 | |
| hfeng-pmm1 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 97.6744 | 99.2727 | 96.1268 | 69.7551 | 819 | 6 | 819 | 33 | 32 | 96.9697 | |
| hfeng-pmm1 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 97.6744 | 99.2727 | 96.1268 | 69.7551 | 819 | 6 | 819 | 33 | 32 | 96.9697 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 96.8134 | 95.9085 | 97.7356 | 69.7525 | 5368 | 229 | 5352 | 124 | 117 | 94.3548 | |
| ckim-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 98.2507 | 97.3988 | 99.1176 | 69.7509 | 337 | 9 | 337 | 3 | 0 | 0.0000 | |
| cchapple-custom | SNP | tv | map_l150_m2_e0 | homalt | 98.3317 | 96.7181 | 100.0000 | 69.7502 | 3949 | 134 | 3947 | 0 | 0 | ||
| ckim-dragen | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.3797 | 99.1736 | 99.5868 | 69.7500 | 240 | 2 | 241 | 1 | 1 | 100.0000 | |
| ndellapenna-hhga | SNP | tv | map_l125_m2_e1 | het | 98.8154 | 98.0195 | 99.6244 | 69.7483 | 10344 | 209 | 10344 | 39 | 16 | 41.0256 | |
| hfeng-pmm3 | SNP | tv | map_l125_m2_e1 | homalt | 99.7612 | 99.7366 | 99.7859 | 69.7479 | 6058 | 16 | 6058 | 13 | 5 | 38.4615 | |
| raldana-dualsentieon | SNP | ti | map_l150_m2_e1 | homalt | 99.6939 | 99.4800 | 99.9086 | 69.7472 | 7653 | 40 | 7653 | 7 | 6 | 85.7143 | |
| anovak-vg | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 92.3819 | 93.7500 | 91.0531 | 69.7462 | 3045 | 203 | 3104 | 305 | 131 | 42.9508 | |
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 98.3957 | 100.0000 | 96.8421 | 69.7452 | 92 | 0 | 92 | 3 | 3 | 100.0000 | |
| ltrigg-rtg1 | INDEL | D1_5 | * | hetalt | 96.8514 | 94.4363 | 99.3932 | 69.7439 | 9675 | 570 | 9828 | 60 | 59 | 98.3333 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 86.9630 | 95.2537 | 80.0000 | 69.7438 | 582 | 29 | 548 | 137 | 132 | 96.3504 | |
| raldana-dualsentieon | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.4907 | 97.7292 | 99.2642 | 69.7423 | 28060 | 652 | 28060 | 208 | 16 | 7.6923 | |
| raldana-dualsentieon | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.4907 | 97.7292 | 99.2642 | 69.7423 | 28060 | 652 | 28060 | 208 | 16 | 7.6923 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 43.4601 | 31.9182 | 68.0775 | 69.7400 | 2684 | 5725 | 2670 | 1252 | 1202 | 96.0064 | |
| dgrover-gatk | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.5326 | 98.2332 | 92.9766 | 69.7368 | 278 | 5 | 278 | 21 | 21 | 100.0000 | |
| rpoplin-dv42 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 99.6481 | 99.5697 | 99.7266 | 69.7354 | 31009 | 134 | 31007 | 85 | 34 | 40.0000 | |
| rpoplin-dv42 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 99.6481 | 99.5697 | 99.7266 | 69.7354 | 31009 | 134 | 31007 | 85 | 34 | 40.0000 | |
| jmaeng-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.7920 | 99.9306 | 99.6537 | 69.7338 | 1439 | 1 | 1439 | 5 | 0 | 0.0000 | |
| cchapple-custom | SNP | tv | map_l150_m2_e1 | homalt | 98.3526 | 96.7586 | 100.0000 | 69.7328 | 4000 | 134 | 3998 | 0 | 0 | ||
| jmaeng-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.6528 | 99.6528 | 99.6528 | 69.7320 | 574 | 2 | 574 | 2 | 2 | 100.0000 | |
| eyeh-varpipe | SNP | ti | map_l100_m1_e0 | het | 99.0514 | 99.6226 | 98.4868 | 69.7302 | 29829 | 113 | 29158 | 448 | 19 | 4.2411 | |
| rpoplin-dv42 | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 99.3569 | 99.3083 | 99.4056 | 69.7301 | 2010 | 14 | 2007 | 12 | 5 | 41.6667 | |
| anovak-vg | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 85.1154 | 90.5013 | 80.3346 | 69.7300 | 30079 | 3157 | 33518 | 8205 | 5776 | 70.3961 | |
| jli-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 98.8764 | 98.8764 | 98.8764 | 69.7279 | 88 | 1 | 88 | 1 | 0 | 0.0000 | |
| ckim-dragen | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.8372 | 100.0000 | 99.6750 | 69.7278 | 914 | 0 | 920 | 3 | 2 | 66.6667 | |
| bgallagher-sentieon | SNP | * | map_l100_m0_e0 | * | 99.1340 | 99.3545 | 98.9146 | 69.7273 | 32629 | 212 | 32625 | 358 | 60 | 16.7598 | |
| rpoplin-dv42 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 98.5075 | 97.0588 | 100.0000 | 69.7248 | 66 | 2 | 66 | 0 | 0 | ||
| jmaeng-gatk | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | * | 99.8449 | 99.7933 | 99.8965 | 69.7243 | 4827 | 10 | 4827 | 5 | 3 | 60.0000 | |
| ghariani-varprowl | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 95.4367 | 99.1065 | 92.0290 | 69.7242 | 2662 | 24 | 2667 | 231 | 0 | 0.0000 | |
| gduggal-snapfb | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 88.4732 | 99.0329 | 79.9484 | 69.7226 | 55093 | 538 | 55477 | 13914 | 538 | 3.8666 | |
| dgrover-gatk | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 99.0037 | 98.8395 | 99.1683 | 69.7220 | 2981 | 35 | 2981 | 25 | 8 | 32.0000 | |
| gduggal-bwafb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 84.1057 | 79.3599 | 89.4551 | 69.7220 | 1711 | 445 | 1773 | 209 | 166 | 79.4258 | |
| gduggal-snapplat | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 61.1186 | 54.5495 | 69.4865 | 69.7213 | 8597 | 7163 | 10095 | 4433 | 1247 | 28.1299 | |
| jmaeng-gatk | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 99.1051 | 98.6148 | 99.6003 | 69.7196 | 1495 | 21 | 1495 | 6 | 3 | 50.0000 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 55.8708 | 55.0239 | 56.7442 | 69.7183 | 115 | 94 | 122 | 93 | 53 | 56.9892 | |
| hfeng-pmm3 | SNP | tv | map_l125_m1_e0 | * | 99.5034 | 99.4568 | 99.5500 | 69.7161 | 15929 | 87 | 15927 | 72 | 10 | 13.8889 | |
| mlin-fermikit | INDEL | D16_PLUS | * | * | 87.3801 | 85.9375 | 88.8720 | 69.7132 | 5830 | 954 | 5846 | 732 | 623 | 85.1093 | |
| raldana-dualsentieon | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.5671 | 100.0000 | 99.1379 | 69.7128 | 230 | 0 | 230 | 2 | 2 | 100.0000 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.0322 | 99.6364 | 96.4789 | 69.7121 | 822 | 3 | 822 | 30 | 29 | 96.6667 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.0322 | 99.6364 | 96.4789 | 69.7121 | 822 | 3 | 822 | 30 | 29 | 96.6667 | |
| jpowers-varprowl | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 46.6236 | 78.3459 | 33.1864 | 69.7120 | 521 | 144 | 527 | 1061 | 1053 | 99.2460 | |
| qzeng-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 98.5178 | 99.1870 | 97.8576 | 69.7090 | 1342 | 11 | 1416 | 31 | 10 | 32.2581 | |