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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
76251-76300 / 86044 show all | |||||||||||||||
| gduggal-snapplat | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 0.0000 | 0.0000 | 0.0000 | 0 | 328 | 0 | 0 | 0 | |||
| bgallagher-sentieon | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 84.8193 | 73.8019 | 99.7033 | 31.3646 | 924 | 328 | 1008 | 3 | 3 | 100.0000 | |
| gduggal-bwaplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 92.5771 | 86.4295 | 99.6662 | 81.9053 | 2089 | 328 | 2090 | 7 | 6 | 85.7143 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 84.1308 | 76.7376 | 93.1005 | 65.8125 | 1082 | 328 | 1093 | 81 | 21 | 25.9259 | |
| ckim-isaac | INDEL | I1_5 | map_siren | homalt | 84.1104 | 72.9373 | 99.3258 | 73.3293 | 884 | 328 | 884 | 6 | 3 | 50.0000 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 76.6987 | 63.3222 | 97.2403 | 40.8261 | 568 | 329 | 599 | 17 | 14 | 82.3529 | |
| mlin-fermikit | INDEL | * | map_l100_m2_e0 | homalt | 77.0808 | 73.9096 | 80.5363 | 81.0585 | 932 | 329 | 931 | 225 | 197 | 87.5556 | |
| ciseli-custom | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 45.6848 | 32.5820 | 76.4151 | 81.0545 | 159 | 329 | 162 | 50 | 35 | 70.0000 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 60.2778 | 43.6644 | 97.2973 | 41.1531 | 255 | 329 | 288 | 8 | 7 | 87.5000 | |
| eyeh-varpipe | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 17.0474 | 9.3664 | 94.7368 | 65.0307 | 34 | 329 | 54 | 3 | 3 | 100.0000 | |
| anovak-vg | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 0.0000 | 3.5191 | 0.0000 | 0.0000 | 12 | 329 | 0 | 0 | 0 | ||
| astatham-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.6432 | 96.0756 | 99.2628 | 61.8299 | 8079 | 330 | 8079 | 60 | 52 | 86.6667 | |
| ltrigg-rtg2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.0316 | 97.6012 | 98.4657 | 62.5780 | 13427 | 330 | 13413 | 209 | 47 | 22.4880 | |
| ltrigg-rtg2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.0316 | 97.6012 | 98.4657 | 62.5780 | 13427 | 330 | 13413 | 209 | 47 | 22.4880 | |
| mlin-fermikit | INDEL | I1_5 | HG002complexvar | hetalt | 88.8775 | 80.8806 | 98.6292 | 68.2274 | 1396 | 330 | 1439 | 20 | 20 | 100.0000 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 93.3394 | 94.5919 | 92.1197 | 68.0226 | 5772 | 330 | 5728 | 490 | 477 | 97.3469 | |
| ndellapenna-hhga | SNP | ti | HG002compoundhet | * | 98.5659 | 98.1119 | 99.0241 | 34.3630 | 17148 | 330 | 17148 | 169 | 140 | 82.8402 | |
| ndellapenna-hhga | SNP | tv | map_siren | het | 99.3169 | 98.8465 | 99.7918 | 55.1017 | 28279 | 330 | 28279 | 59 | 19 | 32.2034 | |
| rpoplin-dv42 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 92.8940 | 87.0028 | 99.6409 | 34.1996 | 2209 | 330 | 2220 | 8 | 8 | 100.0000 | |
| rpoplin-dv42 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 90.6827 | 89.7196 | 91.6667 | 60.0255 | 2880 | 330 | 2871 | 261 | 260 | 99.6169 | |
| ckim-isaac | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 82.8671 | 76.7932 | 89.9844 | 83.5648 | 1092 | 330 | 1150 | 128 | 68 | 53.1250 | |
| gduggal-bwavard | INDEL | I16_PLUS | HG002complexvar | hetalt | 0.0000 | 1.4925 | 0.0000 | 0.0000 | 5 | 330 | 0 | 0 | 0 | ||
| gduggal-bwavard | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 38.9465 | 31.2500 | 51.6729 | 83.5071 | 150 | 330 | 139 | 130 | 89 | 68.4615 | |
| gduggal-bwaplat | INDEL | I1_5 | HG002compoundhet | het | 69.2403 | 61.1765 | 79.7527 | 88.3612 | 520 | 330 | 516 | 131 | 31 | 23.6641 | |
| gduggal-bwaplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 65.0972 | 48.9985 | 96.9512 | 78.2925 | 318 | 331 | 318 | 10 | 5 | 50.0000 | |
| gduggal-bwaplat | INDEL | I1_5 | map_l125_m1_e0 | * | 74.9249 | 60.1205 | 99.4024 | 93.7871 | 499 | 331 | 499 | 3 | 1 | 33.3333 | |
| eyeh-varpipe | SNP | ti | HG002complexvar | het | 99.8630 | 99.8948 | 99.8311 | 17.2379 | 314435 | 331 | 297366 | 503 | 109 | 21.6700 | |
| gduggal-bwaplat | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | * | 62.9139 | 46.2662 | 98.2759 | 80.8707 | 285 | 331 | 285 | 5 | 5 | 100.0000 | |
| raldana-dualsentieon | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 98.2637 | 96.9355 | 99.6289 | 78.1445 | 10470 | 331 | 10470 | 39 | 11 | 28.2051 | |
| anovak-vg | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 49.9912 | 39.7086 | 67.4603 | 80.7634 | 218 | 331 | 255 | 123 | 24 | 19.5122 | |
| anovak-vg | INDEL | I1_5 | map_l125_m2_e0 | * | 59.4733 | 61.3769 | 57.6842 | 87.5801 | 526 | 331 | 548 | 402 | 273 | 67.9104 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.0814 | 91.6918 | 96.5990 | 62.3710 | 3653 | 331 | 3664 | 129 | 115 | 89.1473 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.5229 | 95.1931 | 99.9696 | 26.4607 | 6555 | 331 | 6568 | 2 | 1 | 50.0000 | |
| qzeng-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 95.7239 | 96.8194 | 94.6529 | 42.8294 | 10076 | 331 | 16976 | 959 | 707 | 73.7226 | |
| mlin-fermikit | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 96.5588 | 94.6921 | 98.5005 | 68.4089 | 5905 | 331 | 5912 | 90 | 4 | 4.4444 | |
| ckim-isaac | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 91.8799 | 87.4858 | 96.7387 | 79.1713 | 2314 | 331 | 2373 | 80 | 9 | 11.2500 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 77.4499 | 66.9661 | 91.8256 | 57.9851 | 671 | 331 | 674 | 60 | 42 | 70.0000 | |
| eyeh-varpipe | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 77.1881 | 96.8041 | 64.1824 | 31.3791 | 10026 | 331 | 16242 | 9064 | 9022 | 99.5366 | |
| gduggal-snapplat | INDEL | * | map_l125_m1_e0 | het | 80.6812 | 75.2060 | 87.0161 | 93.7402 | 1004 | 331 | 1079 | 161 | 24 | 14.9068 | |
| ciseli-custom | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 60.0456 | 65.5567 | 55.3892 | 58.1977 | 630 | 331 | 740 | 596 | 423 | 70.9732 | |
| ciseli-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 76.2936 | 79.9879 | 72.9255 | 50.4089 | 1323 | 331 | 1371 | 509 | 198 | 38.8998 | |
| cchapple-custom | SNP | * | map_l150_m0_e0 | het | 94.9871 | 95.8312 | 94.1577 | 84.6817 | 7609 | 331 | 7607 | 472 | 119 | 25.2119 | |
| ckim-isaac | INDEL | * | map_l150_m2_e1 | het | 77.5885 | 64.0693 | 98.3389 | 92.5319 | 592 | 332 | 592 | 10 | 4 | 40.0000 | |
| rpoplin-dv42 | INDEL | * | HG002complexvar | hetalt | 94.3915 | 91.0246 | 98.0170 | 68.2440 | 3367 | 332 | 3460 | 70 | 68 | 97.1429 | |
| rpoplin-dv42 | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 96.9646 | 94.4089 | 99.6626 | 61.7069 | 5606 | 332 | 5612 | 19 | 18 | 94.7368 | |
| jpowers-varprowl | INDEL | I16_PLUS | HG002complexvar | hetalt | 0.0000 | 0.8955 | 0.0000 | 0.0000 | 3 | 332 | 0 | 0 | 0 | ||
| bgallagher-sentieon | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.6669 | 97.8687 | 99.4782 | 72.3688 | 15245 | 332 | 15252 | 80 | 64 | 80.0000 | |
| ghariani-varprowl | INDEL | I16_PLUS | HG002complexvar | hetalt | 0.0000 | 0.8955 | 0.0000 | 0.0000 | 3 | 332 | 0 | 0 | 0 | ||
| hfeng-pmm1 | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 84.6788 | 73.4824 | 99.9005 | 31.7719 | 920 | 332 | 1004 | 1 | 1 | 100.0000 | |
| ghariani-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 49.1300 | 84.7567 | 34.5903 | 59.0099 | 1846 | 332 | 1853 | 3504 | 3453 | 98.5445 | |