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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
23151-23200 / 86044 show all | |||||||||||||||
| ckim-vqsr | SNP | ti | HG002compoundhet | * | 98.9109 | 97.9517 | 99.8891 | 36.4634 | 17120 | 358 | 17120 | 19 | 17 | 89.4737 | |
| asubramanian-gatk | INDEL | D6_15 | HG002compoundhet | * | 94.5808 | 93.8213 | 95.3528 | 36.4670 | 8473 | 558 | 8474 | 413 | 394 | 95.3995 | |
| hfeng-pmm1 | INDEL | I6_15 | HG002compoundhet | * | 94.9235 | 92.7871 | 97.1606 | 36.4711 | 8143 | 633 | 8144 | 238 | 235 | 98.7395 | |
| ckim-gatk | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.7892 | 99.7825 | 99.7959 | 36.4791 | 7339 | 16 | 7335 | 15 | 5 | 33.3333 | |
| gduggal-bwaplat | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | hetalt | 82.0755 | 69.6000 | 100.0000 | 36.4964 | 87 | 38 | 87 | 0 | 0 | ||
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 83.5727 | 82.8140 | 84.3455 | 36.4989 | 15121 | 3138 | 15194 | 2820 | 2630 | 93.2624 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 61.6432 | 97.7532 | 45.0148 | 36.4990 | 2741 | 63 | 2745 | 3353 | 3280 | 97.8228 | |
| anovak-vg | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 65.0593 | 53.4989 | 82.9932 | 36.5011 | 237 | 206 | 244 | 50 | 34 | 68.0000 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 95.4167 | 92.9048 | 98.0682 | 36.5079 | 1532 | 117 | 1726 | 34 | 29 | 85.2941 | |
| hfeng-pmm3 | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 98.1102 | 96.2906 | 100.0000 | 36.5079 | 1246 | 48 | 1360 | 0 | 0 | ||
| mlin-fermikit | SNP | ti | HG002compoundhet | * | 93.7043 | 92.8195 | 94.6061 | 36.5228 | 16223 | 1255 | 16224 | 925 | 739 | 79.8919 | |
| jli-custom | INDEL | I6_15 | * | hetalt | 97.1523 | 94.5503 | 99.9016 | 36.5262 | 8085 | 466 | 8123 | 8 | 8 | 100.0000 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 92.9480 | 87.0130 | 99.7519 | 36.5354 | 402 | 60 | 402 | 1 | 1 | 100.0000 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 50.4505 | 33.7349 | 100.0000 | 36.5385 | 28 | 55 | 33 | 0 | 0 | ||
| anovak-vg | SNP | tv | tech_badpromoters | homalt | 93.1507 | 87.1795 | 100.0000 | 36.5385 | 34 | 5 | 33 | 0 | 0 | ||
| jpowers-varprowl | INDEL | D16_PLUS | HG002compoundhet | * | 17.0370 | 14.9082 | 19.8751 | 36.5405 | 349 | 1992 | 350 | 1411 | 1404 | 99.5039 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 63.1996 | 46.4567 | 98.8107 | 36.5459 | 3304 | 3808 | 2908 | 35 | 31 | 88.5714 | |
| jmaeng-gatk | INDEL | I6_15 | HG002compoundhet | * | 93.8901 | 92.0123 | 95.8462 | 36.5464 | 8075 | 701 | 8076 | 350 | 348 | 99.4286 | |
| mlin-fermikit | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | het | 98.0340 | 96.7727 | 99.3285 | 36.5490 | 2069 | 69 | 2071 | 14 | 0 | 0.0000 | |
| ckim-gatk | SNP | * | func_cds | het | 99.5225 | 99.9283 | 99.1199 | 36.5539 | 11153 | 8 | 11150 | 99 | 1 | 1.0101 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 94.8382 | 95.5706 | 94.1169 | 36.5552 | 1273 | 59 | 7679 | 480 | 470 | 97.9167 | |
| eyeh-varpipe | INDEL | * | func_cds | het | 93.8679 | 92.9907 | 94.7619 | 36.5559 | 199 | 15 | 199 | 11 | 9 | 81.8182 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 49.3741 | 54.9918 | 44.7978 | 36.5595 | 336 | 275 | 831 | 1024 | 846 | 82.6172 | |
| anovak-vg | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 53.2015 | 46.3732 | 62.3880 | 36.5667 | 748 | 865 | 4039 | 2435 | 1935 | 79.4661 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.5119 | 97.7585 | 99.2769 | 36.5690 | 9246 | 212 | 9199 | 67 | 51 | 76.1194 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 93.8528 | 89.4478 | 98.7142 | 36.5693 | 2365 | 279 | 2380 | 31 | 29 | 93.5484 | |
| ltrigg-rtg2 | INDEL | * | func_cds | * | 99.3248 | 99.1011 | 99.5495 | 36.5714 | 441 | 4 | 442 | 2 | 0 | 0.0000 | |
| ltrigg-rtg1 | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 95.4970 | 92.3077 | 98.9145 | 36.5749 | 732 | 61 | 729 | 8 | 8 | 100.0000 | |
| ckim-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.1399 | 92.8943 | 99.6204 | 36.5756 | 15518 | 1187 | 15746 | 60 | 60 | 100.0000 | |
| ckim-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.1399 | 92.8943 | 99.6204 | 36.5756 | 15518 | 1187 | 15746 | 60 | 60 | 100.0000 | |
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.1302 | 92.8764 | 99.6203 | 36.5800 | 15515 | 1190 | 15743 | 60 | 60 | 100.0000 | |
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.1302 | 92.8764 | 99.6203 | 36.5800 | 15515 | 1190 | 15743 | 60 | 60 | 100.0000 | |
| hfeng-pmm1 | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 100.0000 | 100.0000 | 100.0000 | 36.5834 | 3987 | 0 | 3987 | 0 | 0 | ||
| ckim-isaac | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 93.1339 | 90.7869 | 95.6056 | 36.5855 | 10061 | 1021 | 9986 | 459 | 410 | 89.3246 | |
| anovak-vg | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 60.1585 | 64.6439 | 56.2551 | 36.6040 | 9449 | 5168 | 18693 | 14536 | 11429 | 78.6255 | |
| ckim-vqsr | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.5978 | 99.3202 | 99.8769 | 36.6057 | 7305 | 50 | 7301 | 9 | 4 | 44.4444 | |
| jmaeng-gatk | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.7576 | 99.6772 | 99.8383 | 36.6060 | 2470 | 8 | 2469 | 4 | 0 | 0.0000 | |
| egarrison-hhga | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.6287 | 99.4366 | 99.8215 | 36.6123 | 6707 | 38 | 6709 | 12 | 10 | 83.3333 | |
| ndellapenna-hhga | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 63.4096 | 46.8051 | 98.2726 | 36.6180 | 586 | 666 | 512 | 9 | 6 | 66.6667 | |
| ltrigg-rtg2 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.9977 | 96.8112 | 99.2136 | 36.6279 | 759 | 25 | 757 | 6 | 6 | 100.0000 | |
| jmaeng-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 95.8097 | 92.2658 | 99.6368 | 36.6287 | 15413 | 1292 | 15635 | 57 | 57 | 100.0000 | |
| jmaeng-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 95.8097 | 92.2658 | 99.6368 | 36.6287 | 15413 | 1292 | 15635 | 57 | 57 | 100.0000 | |
| mlin-fermikit | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 76.0030 | 61.7352 | 98.8481 | 36.6332 | 1352 | 838 | 1373 | 16 | 16 | 100.0000 | |
| ckim-gatk | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.8184 | 99.8386 | 99.7982 | 36.6402 | 2474 | 4 | 2473 | 5 | 1 | 20.0000 | |
| qzeng-custom | INDEL | I6_15 | HG002compoundhet | * | 75.9258 | 69.2571 | 84.0157 | 36.6439 | 6078 | 2698 | 5992 | 1140 | 884 | 77.5439 | |
| jlack-gatk | SNP | * | func_cds | het | 98.8875 | 99.9731 | 97.8251 | 36.6500 | 11158 | 3 | 11155 | 248 | 1 | 0.4032 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 83.6943 | 72.8549 | 98.3229 | 36.6534 | 467 | 174 | 469 | 8 | 6 | 75.0000 | |
| ckim-dragen | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.5338 | 99.7378 | 97.3585 | 36.6570 | 7228 | 19 | 7224 | 196 | 195 | 99.4898 | |
| cchapple-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.6494 | 97.0713 | 98.2344 | 36.6573 | 9181 | 277 | 10015 | 180 | 172 | 95.5556 | |
| jli-custom | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.6524 | 99.7101 | 99.5947 | 36.6587 | 3440 | 10 | 3440 | 14 | 2 | 14.2857 | |