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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
73251-73300 / 86044 show all | |||||||||||||||
| jlack-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 96.6125 | 96.9110 | 96.3159 | 71.1607 | 3451 | 110 | 3451 | 132 | 77 | 58.3333 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 96.1590 | 93.4295 | 99.0528 | 42.4608 | 2915 | 205 | 3451 | 33 | 31 | 93.9394 | |
| ckim-vqsr | SNP | ti | map_l150_m0_e0 | * | 60.7533 | 43.9130 | 98.5441 | 93.9394 | 3452 | 4409 | 3452 | 51 | 0 | 0.0000 | |
| rpoplin-dv42 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 92.9690 | 88.5553 | 97.8458 | 55.3644 | 3451 | 446 | 3452 | 76 | 71 | 93.4211 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 93.9836 | 91.7841 | 96.2911 | 69.5456 | 3452 | 309 | 3453 | 133 | 125 | 93.9850 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 93.9836 | 91.7841 | 96.2911 | 69.5456 | 3452 | 309 | 3453 | 133 | 125 | 93.9850 | |
| ckim-dragen | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.7253 | 99.7681 | 99.6824 | 38.1649 | 3442 | 8 | 3453 | 11 | 4 | 36.3636 | |
| ltrigg-rtg2 | INDEL | D1_5 | map_siren | * | 98.7460 | 98.3565 | 99.1387 | 75.8494 | 3471 | 58 | 3453 | 30 | 4 | 13.3333 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 95.9082 | 98.0492 | 93.8587 | 69.1405 | 3468 | 69 | 3454 | 226 | 220 | 97.3451 | |
| gduggal-bwafb | INDEL | D1_5 | map_siren | * | 98.1690 | 98.0164 | 98.3220 | 81.5743 | 3459 | 70 | 3457 | 59 | 15 | 25.4237 | |
| ltrigg-rtg2 | INDEL | * | map_l100_m1_e0 | * | 97.6819 | 96.3469 | 99.0544 | 78.3512 | 3455 | 131 | 3457 | 33 | 4 | 12.1212 | |
| hfeng-pmm3 | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.0292 | 97.0795 | 98.9977 | 67.6517 | 3457 | 104 | 3457 | 35 | 30 | 85.7143 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.9326 | 97.1076 | 98.7718 | 67.6791 | 3458 | 103 | 3458 | 43 | 30 | 69.7674 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.5183 | 97.1076 | 97.9326 | 72.3189 | 3458 | 103 | 3458 | 73 | 57 | 78.0822 | |
| ndellapenna-hhga | INDEL | D6_15 | * | hetalt | 65.7378 | 49.3394 | 98.4629 | 43.6387 | 4033 | 4141 | 3459 | 54 | 41 | 75.9259 | |
| ckim-isaac | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 96.4258 | 95.4620 | 97.4092 | 41.9487 | 3492 | 166 | 3459 | 92 | 56 | 60.8696 | |
| rpoplin-dv42 | INDEL | * | HG002complexvar | hetalt | 94.3915 | 91.0246 | 98.0170 | 68.2440 | 3367 | 332 | 3460 | 70 | 68 | 97.1429 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 96.9627 | 94.4899 | 99.5685 | 38.0503 | 3464 | 202 | 3461 | 15 | 9 | 60.0000 | |
| ckim-vqsr | INDEL | D1_5 | map_siren | * | 98.3083 | 97.9031 | 98.7169 | 84.9543 | 3455 | 74 | 3462 | 45 | 6 | 13.3333 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 93.1275 | 89.5499 | 97.0028 | 61.5094 | 5133 | 599 | 3463 | 107 | 92 | 85.9813 | |
| qzeng-custom | SNP | * | map_l250_m2_e1 | het | 76.4225 | 66.2804 | 90.2293 | 96.3549 | 3489 | 1775 | 3463 | 375 | 310 | 82.6667 | |
| mlin-fermikit | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 79.3723 | 90.3851 | 70.7516 | 51.9765 | 3497 | 372 | 3464 | 1432 | 1427 | 99.6508 | |
| ghariani-varprowl | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 94.6830 | 99.7395 | 90.1145 | 68.5511 | 3446 | 9 | 3464 | 380 | 233 | 61.3158 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 94.5739 | 94.2717 | 94.8781 | 48.0950 | 3456 | 210 | 3464 | 187 | 150 | 80.2139 | |
| jpowers-varprowl | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 94.4249 | 99.7395 | 89.6480 | 70.2838 | 3446 | 9 | 3464 | 400 | 231 | 57.7500 | |
| hfeng-pmm1 | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 94.1710 | 92.9950 | 95.3770 | 77.2463 | 3757 | 283 | 3466 | 168 | 128 | 76.1905 | |
| mlin-fermikit | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 95.2599 | 99.8263 | 91.0930 | 68.6491 | 3449 | 6 | 3467 | 339 | 278 | 82.0059 | |
| ndellapenna-hhga | INDEL | D1_5 | map_siren | * | 98.3828 | 98.2715 | 98.4943 | 79.4152 | 3468 | 61 | 3467 | 53 | 28 | 52.8302 | |
| hfeng-pmm1 | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 92.9701 | 86.9508 | 99.8848 | 40.2923 | 3325 | 499 | 3468 | 4 | 4 | 100.0000 | |
| ckim-vqsr | INDEL | * | map_l100_m1_e0 | * | 97.1981 | 96.6815 | 97.7202 | 88.7691 | 3467 | 119 | 3472 | 81 | 16 | 19.7531 | |
| asubramanian-gatk | SNP | tv | map_l125_m2_e0 | het | 49.8851 | 33.2599 | 99.7415 | 93.1706 | 3473 | 6969 | 3472 | 9 | 2 | 22.2222 | |
| bgallagher-sentieon | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 92.8385 | 87.0031 | 99.5129 | 39.9105 | 3327 | 497 | 3473 | 17 | 16 | 94.1176 | |
| ghariani-varprowl | INDEL | * | map_l100_m2_e1 | * | 90.3178 | 92.5453 | 88.1950 | 92.4782 | 3476 | 280 | 3474 | 465 | 216 | 46.4516 | |
| ckim-dragen | INDEL | D1_5 | map_siren | * | 98.3320 | 98.6115 | 98.0541 | 82.6974 | 3480 | 49 | 3477 | 69 | 7 | 10.1449 | |
| hfeng-pmm2 | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 93.1791 | 87.3169 | 99.8851 | 40.5059 | 3339 | 485 | 3477 | 4 | 4 | 100.0000 | |
| ckim-dragen | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 92.8661 | 87.0293 | 99.5422 | 40.0515 | 3328 | 496 | 3479 | 16 | 16 | 100.0000 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 63.1837 | 91.9278 | 48.1333 | 41.9722 | 3462 | 304 | 3481 | 3751 | 3650 | 97.3074 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 63.1837 | 91.9278 | 48.1333 | 41.9722 | 3462 | 304 | 3481 | 3751 | 3650 | 97.3074 | |
| egarrison-hhga | INDEL | D1_5 | map_siren | * | 98.6263 | 98.6682 | 98.5844 | 80.4104 | 3482 | 47 | 3482 | 50 | 22 | 44.0000 | |
| ciseli-custom | INDEL | * | map_siren | het | 76.8656 | 76.7303 | 77.0013 | 84.6311 | 3459 | 1049 | 3482 | 1040 | 630 | 60.5769 | |
| rpoplin-dv42 | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 98.9624 | 98.4167 | 99.5141 | 71.6519 | 3481 | 56 | 3482 | 17 | 15 | 88.2353 | |
| ndellapenna-hhga | INDEL | * | map_l100_m1_e0 | * | 97.2875 | 96.9325 | 97.6451 | 97.5899 | 3476 | 110 | 3483 | 84 | 38 | 45.2381 | |
| jmaeng-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.0298 | 97.8096 | 98.2511 | 71.9586 | 3483 | 78 | 3483 | 62 | 54 | 87.0968 | |
| ckim-dragen | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.6321 | 97.8377 | 97.4273 | 73.5072 | 3484 | 77 | 3484 | 92 | 64 | 69.5652 | |
| cchapple-custom | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.0646 | 99.1518 | 98.9776 | 67.7712 | 3507 | 30 | 3485 | 36 | 36 | 100.0000 | |
| ckim-dragen | INDEL | * | map_l100_m1_e0 | * | 96.9560 | 97.3229 | 96.5919 | 86.1888 | 3490 | 96 | 3486 | 123 | 19 | 15.4472 | |
| gduggal-bwaplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 68.0328 | 54.2991 | 91.0658 | 88.7322 | 3486 | 2934 | 3486 | 342 | 80 | 23.3918 | |
| gduggal-bwaplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 68.0328 | 54.2991 | 91.0658 | 88.7322 | 3486 | 2934 | 3486 | 342 | 80 | 23.3918 | |
| hfeng-pmm1 | INDEL | D1_5 | map_siren | * | 99.0467 | 98.5832 | 99.5147 | 78.4947 | 3479 | 50 | 3486 | 17 | 2 | 11.7647 | |
| mlin-fermikit | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 96.9189 | 96.4670 | 97.3750 | 70.9358 | 3495 | 128 | 3487 | 94 | 86 | 91.4894 | |