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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
14101-14150 / 86044 show all | |||||||||||||||
| ckim-gatk | SNP | ti | map_l100_m1_e0 | homalt | 84.4316 | 73.0902 | 99.9391 | 65.0795 | 13127 | 4833 | 13127 | 8 | 7 | 87.5000 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.8747 | 99.8104 | 99.9390 | 55.0186 | 14742 | 28 | 14744 | 9 | 4 | 44.4444 | |
| hfeng-pmm1 | SNP | * | HG002compoundhet | het | 96.0618 | 92.4743 | 99.9390 | 43.1383 | 13111 | 1067 | 13110 | 8 | 4 | 50.0000 | |
| jli-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.8713 | 99.8037 | 99.9390 | 54.3200 | 14741 | 29 | 14742 | 9 | 4 | 44.4444 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.8950 | 99.8510 | 99.9390 | 54.8240 | 14748 | 22 | 14750 | 9 | 4 | 44.4444 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.7762 | 99.6141 | 99.9389 | 56.2917 | 14713 | 57 | 14715 | 9 | 1 | 11.1111 | |
| raldana-dualsentieon | SNP | * | * | * | 99.9260 | 99.9131 | 99.9389 | 18.4181 | 3051965 | 2654 | 3051826 | 1867 | 97 | 5.1955 | |
| ckim-dragen | SNP | ti | HG002complexvar | * | 99.9317 | 99.9245 | 99.9389 | 17.8695 | 508052 | 384 | 508287 | 311 | 156 | 50.1608 | |
| jmaeng-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.5044 | 99.0738 | 99.9389 | 63.8841 | 11445 | 107 | 11445 | 7 | 7 | 100.0000 | |
| jmaeng-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.5044 | 99.0738 | 99.9389 | 63.8841 | 11445 | 107 | 11445 | 7 | 7 | 100.0000 | |
| jli-custom | SNP | * | map_l100_m2_e1 | homalt | 99.7946 | 99.6510 | 99.9387 | 59.6958 | 27699 | 97 | 27699 | 17 | 16 | 94.1176 | |
| ndellapenna-hhga | SNP | ti | HG002complexvar | * | 99.8069 | 99.6755 | 99.9387 | 17.4775 | 506786 | 1650 | 506808 | 311 | 223 | 71.7042 | |
| ndellapenna-hhga | SNP | ti | map_l125_m2_e1 | homalt | 99.7508 | 99.5636 | 99.9387 | 67.6903 | 11408 | 50 | 11408 | 7 | 7 | 100.0000 | |
| jli-custom | SNP | ti | map_l100_m1_e0 | homalt | 99.7965 | 99.6548 | 99.9386 | 56.4067 | 17898 | 62 | 17898 | 11 | 11 | 100.0000 | |
| ltrigg-rtg2 | SNP | ti | map_l100_m1_e0 | homalt | 99.8049 | 99.6715 | 99.9386 | 57.1476 | 17901 | 59 | 17900 | 11 | 11 | 100.0000 | |
| raldana-dualsentieon | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 94.8996 | 90.3444 | 99.9384 | 37.7684 | 1600 | 171 | 1622 | 1 | 1 | 100.0000 | |
| ckim-vqsr | SNP | tv | map_l125_m1_e0 | homalt | 43.3097 | 27.6451 | 99.9383 | 87.2272 | 1620 | 4240 | 1620 | 1 | 0 | 0.0000 | |
| raldana-dualsentieon | INDEL | I1_5 | HG002complexvar | hetalt | 94.9524 | 90.4403 | 99.9382 | 69.6987 | 1561 | 165 | 1618 | 1 | 1 | 100.0000 | |
| ndellapenna-hhga | SNP | * | map_siren | homalt | 99.8258 | 99.7135 | 99.9382 | 52.6378 | 54998 | 158 | 54999 | 34 | 30 | 88.2353 | |
| ndellapenna-hhga | SNP | ti | map_l125_m2_e0 | homalt | 99.7486 | 99.5598 | 99.9381 | 67.6520 | 11308 | 50 | 11308 | 7 | 7 | 100.0000 | |
| jli-custom | SNP | * | map_l100_m2_e0 | homalt | 99.7944 | 99.6512 | 99.9381 | 59.7123 | 27427 | 96 | 27427 | 17 | 16 | 94.1176 | |
| ckim-gatk | SNP | ti | map_l100_m0_e0 | homalt | 76.7317 | 62.2717 | 99.9381 | 70.4634 | 4841 | 2933 | 4841 | 3 | 2 | 66.6667 | |
| ckim-dragen | SNP | * | HG002complexvar | * | 99.9301 | 99.9223 | 99.9379 | 19.4552 | 753795 | 586 | 754278 | 469 | 236 | 50.3198 | |
| gduggal-bwavard | SNP | * | HG002complexvar | homalt | 98.4291 | 96.9651 | 99.9379 | 18.6318 | 279817 | 8758 | 270523 | 168 | 110 | 65.4762 | |
| ckim-vqsr | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | * | 99.7826 | 99.6279 | 99.9378 | 69.6768 | 4819 | 18 | 4819 | 3 | 3 | 100.0000 | |
| jli-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.9067 | 99.8757 | 99.9378 | 47.2268 | 1607 | 2 | 1607 | 1 | 1 | 100.0000 | |
| hfeng-pmm3 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.8756 | 99.8135 | 99.9378 | 52.0442 | 1606 | 3 | 1606 | 1 | 0 | 0.0000 | |
| hfeng-pmm2 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.8756 | 99.8135 | 99.9378 | 53.0803 | 1606 | 3 | 1606 | 1 | 0 | 0.0000 | |
| astatham-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.8445 | 99.7514 | 99.9377 | 43.3110 | 1605 | 4 | 1605 | 1 | 1 | 100.0000 | |
| ckim-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.8445 | 99.7514 | 99.9377 | 43.4109 | 1605 | 4 | 1605 | 1 | 1 | 100.0000 | |
| dgrover-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.8445 | 99.7514 | 99.9377 | 43.6886 | 1605 | 4 | 1605 | 1 | 1 | 100.0000 | |
| astatham-gatk | INDEL | I6_15 | * | hetalt | 96.4480 | 93.1938 | 99.9376 | 38.5683 | 7969 | 582 | 8010 | 5 | 5 | 100.0000 | |
| ckim-vqsr | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.6885 | 99.4406 | 99.9375 | 43.4875 | 1600 | 9 | 1600 | 1 | 1 | 100.0000 | |
| gduggal-snapvard | SNP | ti | * | homalt | 99.4493 | 98.9663 | 99.9370 | 16.0694 | 794738 | 8301 | 790421 | 498 | 326 | 65.4618 | |
| ckim-isaac | SNP | * | map_l125_m0_e0 | homalt | 64.1166 | 47.1990 | 99.9369 | 61.5104 | 3168 | 3544 | 3168 | 2 | 2 | 100.0000 | |
| hfeng-pmm2 | SNP | * | * | het | 99.9111 | 99.8854 | 99.9369 | 19.2150 | 1871439 | 2148 | 1871315 | 1181 | 42 | 3.5563 | |
| jli-custom | SNP | * | map_l100_m1_e0 | homalt | 99.7923 | 99.6482 | 99.9369 | 57.0814 | 26908 | 95 | 26908 | 17 | 16 | 94.1176 | |
| jli-custom | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.8148 | 99.6933 | 99.9367 | 55.5774 | 11050 | 34 | 11048 | 7 | 4 | 57.1429 | |
| rpoplin-dv42 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.9684 | 100.0000 | 99.9367 | 49.1803 | 1580 | 0 | 1580 | 1 | 0 | 0.0000 | |
| hfeng-pmm3 | SNP | ti | map_siren | homalt | 99.9129 | 99.8892 | 99.9367 | 51.9265 | 37874 | 42 | 37868 | 24 | 14 | 58.3333 | |
| ckim-gatk | SNP | * | map_l125_m2_e1 | homalt | 77.2853 | 63.0048 | 99.9367 | 76.2699 | 11046 | 6486 | 11046 | 7 | 4 | 57.1429 | |
| ckim-gatk | SNP | * | map_l150_m1_e0 | homalt | 71.6189 | 55.8059 | 99.9365 | 80.2510 | 6291 | 4982 | 6291 | 4 | 2 | 50.0000 | |
| ltrigg-rtg1 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 99.6201 | 99.3057 | 99.9365 | 31.9250 | 4720 | 33 | 4718 | 3 | 3 | 100.0000 | |
| astatham-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.7464 | 99.5570 | 99.9365 | 52.5475 | 1573 | 7 | 1573 | 1 | 0 | 0.0000 | |
| ltrigg-rtg1 | SNP | * | map_siren | homalt | 99.8648 | 99.7933 | 99.9364 | 52.2080 | 55042 | 114 | 55031 | 35 | 31 | 88.5714 | |
| hfeng-pmm1 | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.4409 | 98.9502 | 99.9364 | 58.3709 | 55047 | 584 | 55037 | 35 | 12 | 34.2857 | |
| ndellapenna-hhga | SNP | ti | map_l125_m1_e0 | homalt | 99.7415 | 99.5473 | 99.9364 | 64.8588 | 10995 | 50 | 10995 | 7 | 7 | 100.0000 | |
| dgrover-gatk | SNP | ti | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.9282 | 99.9202 | 99.9362 | 44.6182 | 6263 | 5 | 6263 | 4 | 3 | 75.0000 | |
| gduggal-snapplat | SNP | * | map_l125_m2_e1 | homalt | 94.3221 | 89.3053 | 99.9361 | 69.8871 | 15657 | 1875 | 15646 | 10 | 9 | 90.0000 | |
| hfeng-pmm3 | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.7891 | 99.6426 | 99.9361 | 57.3259 | 28159 | 101 | 28161 | 18 | 11 | 61.1111 | |