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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
58801-58850 / 86044 show all | |||||||||||||||
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 85.0825 | 75.8761 | 96.8314 | 49.6990 | 18620 | 5920 | 18611 | 609 | 395 | 64.8604 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.5630 | 99.4272 | 99.6991 | 49.6904 | 3645 | 21 | 3645 | 11 | 11 | 100.0000 | |
| gduggal-snapvard | SNP | ti | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 98.6335 | 98.6470 | 98.6200 | 49.6901 | 4010 | 55 | 4002 | 56 | 5 | 8.9286 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.0155 | 96.3678 | 99.7204 | 49.6879 | 30830 | 1162 | 31028 | 87 | 75 | 86.2069 | |
| gduggal-snapfb | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | * | 91.9883 | 99.2888 | 85.6879 | 49.6867 | 7399 | 53 | 7430 | 1241 | 43 | 3.4650 | |
| dgrover-gatk | SNP | * | tech_badpromoters | * | 98.4026 | 98.0892 | 98.7179 | 49.6774 | 154 | 3 | 154 | 2 | 2 | 100.0000 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 84.8057 | 94.4882 | 76.9231 | 49.6774 | 120 | 7 | 120 | 36 | 30 | 83.3333 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 55.5615 | 38.9075 | 97.1429 | 49.6732 | 349 | 548 | 374 | 11 | 11 | 100.0000 | |
| raldana-dualsentieon | SNP | * | map_siren | homalt | 99.8920 | 99.8187 | 99.9655 | 49.6673 | 55056 | 100 | 55047 | 19 | 19 | 100.0000 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 88.0210 | 92.7552 | 83.7467 | 49.6639 | 2535 | 198 | 2195 | 426 | 362 | 84.9765 | |
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.1094 | 95.4346 | 98.8440 | 49.6543 | 14110 | 675 | 14108 | 165 | 157 | 95.1515 | |
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 90.4630 | 88.1350 | 92.9173 | 49.6530 | 2429 | 327 | 2427 | 185 | 180 | 97.2973 | |
| raldana-dualsentieon | SNP | tv | tech_badpromoters | * | 97.9021 | 97.2222 | 98.5915 | 49.6454 | 70 | 2 | 70 | 1 | 1 | 100.0000 | |
| hfeng-pmm1 | SNP | tv | tech_badpromoters | * | 99.3007 | 98.6111 | 100.0000 | 49.6454 | 71 | 1 | 71 | 0 | 0 | ||
| ltrigg-rtg1 | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 92.1710 | 86.1140 | 99.1445 | 49.6360 | 3293 | 531 | 3361 | 29 | 28 | 96.5517 | |
| gduggal-bwafb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 89.5071 | 83.4165 | 96.5571 | 49.6329 | 11705 | 2327 | 3113 | 111 | 109 | 98.1982 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 100.0000 | 100.0000 | 100.0000 | 49.6307 | 343 | 0 | 341 | 0 | 0 | ||
| jmaeng-gatk | SNP | tv | HG002compoundhet | * | 99.2678 | 98.7672 | 99.7735 | 49.6292 | 8813 | 110 | 8810 | 20 | 17 | 85.0000 | |
| rpoplin-dv42 | INDEL | I6_15 | * | * | 96.3018 | 94.7670 | 97.8872 | 49.6208 | 23524 | 1299 | 23536 | 508 | 491 | 96.6535 | |
| jpowers-varprowl | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 46.8416 | 83.8718 | 32.4948 | 49.6168 | 3245 | 624 | 3268 | 6789 | 6766 | 99.6612 | |
| gduggal-bwavard | SNP | * | HG002compoundhet | het | 83.4515 | 85.5762 | 81.4296 | 49.6147 | 12133 | 2045 | 13203 | 3011 | 2546 | 84.5566 | |
| gduggal-snapvard | INDEL | D6_15 | * | het | 75.6496 | 85.7660 | 67.6679 | 49.6050 | 9942 | 1650 | 14418 | 6889 | 5530 | 80.2729 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 75.1496 | 77.5758 | 72.8707 | 49.6025 | 256 | 74 | 231 | 86 | 83 | 96.5116 | |
| gduggal-snapvard | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 53.1638 | 65.0431 | 44.9536 | 49.5979 | 1282 | 689 | 3296 | 4036 | 3328 | 82.4579 | |
| gduggal-snapvard | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 53.1638 | 65.0431 | 44.9536 | 49.5979 | 1282 | 689 | 3296 | 4036 | 3328 | 82.4579 | |
| gduggal-snapvard | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | het | 95.2056 | 96.5856 | 93.8645 | 49.5961 | 2065 | 73 | 2050 | 134 | 7 | 5.2239 | |
| gduggal-bwafb | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 99.6580 | 99.3861 | 99.9314 | 49.5848 | 1457 | 9 | 1456 | 1 | 0 | 0.0000 | |
| hfeng-pmm1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.1042 | 96.9367 | 99.3002 | 49.5751 | 31012 | 980 | 30935 | 218 | 193 | 88.5321 | |
| ckim-isaac | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 93.3376 | 91.6367 | 95.1028 | 49.5731 | 10179 | 929 | 9943 | 512 | 284 | 55.4688 | |
| asubramanian-gatk | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.4277 | 98.8814 | 99.9800 | 49.5688 | 9989 | 113 | 9998 | 2 | 2 | 100.0000 | |
| gduggal-bwavard | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 29.1765 | 45.9259 | 21.3793 | 49.5652 | 62 | 73 | 62 | 228 | 224 | 98.2456 | |
| hfeng-pmm3 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.0454 | 96.7804 | 99.3438 | 49.5652 | 30962 | 1030 | 30885 | 204 | 187 | 91.6667 | |
| ckim-isaac | INDEL | I1_5 | * | * | 96.6542 | 94.9085 | 98.4652 | 49.5628 | 142993 | 7671 | 142942 | 2228 | 1638 | 73.5189 | |
| qzeng-custom | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.1042 | 99.4409 | 98.7698 | 49.5614 | 10672 | 60 | 10678 | 133 | 13 | 9.7744 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 33.7398 | 28.1768 | 42.0398 | 49.5609 | 102 | 260 | 169 | 233 | 185 | 79.3991 | |
| ckim-vqsr | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.7260 | 99.8005 | 99.6515 | 49.5605 | 4003 | 8 | 4003 | 14 | 2 | 14.2857 | |
| ltrigg-rtg1 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.6765 | 99.9590 | 99.3956 | 49.5528 | 2438 | 1 | 2467 | 15 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | I6_15 | * | * | 97.8954 | 96.7812 | 99.0356 | 49.5509 | 24024 | 799 | 24029 | 234 | 222 | 94.8718 | |
| cchapple-custom | INDEL | I6_15 | * | het | 98.6365 | 97.9268 | 99.3566 | 49.5505 | 9825 | 208 | 19457 | 126 | 91 | 72.2222 | |
| ltrigg-rtg1 | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.2071 | 90.0993 | 98.7075 | 49.5392 | 3540 | 389 | 3513 | 46 | 33 | 71.7391 | |
| ckim-dragen | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.6954 | 99.6733 | 99.7175 | 49.5386 | 6711 | 22 | 6707 | 19 | 12 | 63.1579 | |
| ckim-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.7261 | 99.8504 | 99.6021 | 49.5356 | 4005 | 6 | 4005 | 16 | 2 | 12.5000 | |
| ltrigg-rtg2 | INDEL | I6_15 | HG002complexvar | het | 98.2137 | 97.4098 | 99.0310 | 49.5355 | 2294 | 61 | 2044 | 20 | 9 | 45.0000 | |
| ghariani-varprowl | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 31.8050 | 60.7407 | 21.5426 | 49.5302 | 82 | 53 | 81 | 295 | 292 | 98.9831 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 96.8247 | 99.2858 | 94.4828 | 49.5258 | 9453 | 68 | 9453 | 552 | 547 | 99.0942 | |
| gduggal-bwafb | INDEL | D16_PLUS | * | het | 87.0129 | 80.9433 | 94.0664 | 49.5246 | 2557 | 602 | 3995 | 252 | 244 | 96.8254 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 90.7313 | 91.0661 | 90.3989 | 49.5222 | 6116 | 600 | 6685 | 710 | 208 | 29.2958 | |
| jmaeng-gatk | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.8563 | 99.7624 | 99.9504 | 49.5168 | 10078 | 24 | 10078 | 5 | 5 | 100.0000 | |
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 94.8193 | 92.4187 | 97.3479 | 49.5090 | 2755 | 226 | 2753 | 75 | 52 | 69.3333 | |
| gduggal-snapvard | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 50.1574 | 67.0715 | 40.0560 | 49.5050 | 497 | 244 | 1573 | 2354 | 1678 | 71.2829 | |