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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
21201-21250 / 86044 show all | |||||||||||||||
| cchapple-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 96.7502 | 94.8052 | 98.7768 | 42.3619 | 365 | 20 | 969 | 12 | 7 | 58.3333 | |
| astatham-gatk | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.4245 | 98.9414 | 99.9124 | 64.7733 | 27385 | 293 | 27376 | 24 | 14 | 58.3333 | |
| anovak-vg | INDEL | D6_15 | map_l150_m1_e0 | het | 80.3240 | 87.1795 | 74.4681 | 92.3948 | 34 | 5 | 35 | 12 | 7 | 58.3333 | |
| anovak-vg | INDEL | D6_15 | map_l150_m2_e0 | het | 79.4212 | 82.6087 | 76.4706 | 92.2844 | 38 | 8 | 39 | 12 | 7 | 58.3333 | |
| anovak-vg | INDEL | D6_15 | map_l150_m2_e1 | het | 79.8362 | 82.9787 | 76.9231 | 92.2619 | 39 | 8 | 40 | 12 | 7 | 58.3333 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.8892 | 97.3753 | 98.4085 | 66.7402 | 742 | 20 | 742 | 12 | 7 | 58.3333 | |
| astatham-gatk | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.4739 | 99.3445 | 99.6037 | 78.1364 | 6062 | 40 | 6032 | 24 | 14 | 58.3333 | |
| astatham-gatk | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 99.0488 | 98.3627 | 99.7446 | 66.6690 | 4686 | 78 | 4686 | 12 | 7 | 58.3333 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 80.0966 | 67.4532 | 98.5731 | 65.2719 | 2487 | 1200 | 2487 | 36 | 21 | 58.3333 | |
| anovak-vg | INDEL | I1_5 | HG002complexvar | het | 44.4856 | 30.2381 | 84.1220 | 66.7223 | 5500 | 12689 | 6204 | 1171 | 683 | 58.3262 | |
| ckim-isaac | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 96.5147 | 94.2784 | 98.8597 | 54.0704 | 52448 | 3183 | 52797 | 609 | 355 | 58.2923 | |
| rpoplin-dv42 | SNP | * | map_siren | * | 99.6224 | 99.5097 | 99.7354 | 54.5067 | 145511 | 717 | 145497 | 386 | 225 | 58.2902 | |
| gduggal-snapplat | SNP | ti | map_l150_m0_e0 | * | 90.2459 | 86.2613 | 94.6165 | 87.8341 | 6781 | 1080 | 6784 | 386 | 225 | 58.2902 | |
| anovak-vg | INDEL | * | map_l100_m0_e0 | * | 72.6539 | 73.0006 | 72.3105 | 87.1262 | 1141 | 422 | 1183 | 453 | 264 | 58.2781 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 85.5522 | 92.4908 | 79.5820 | 75.9660 | 505 | 41 | 495 | 127 | 74 | 58.2677 | |
| ciseli-custom | INDEL | D6_15 | map_l100_m1_e0 | * | 53.8462 | 51.5504 | 56.3559 | 88.4200 | 133 | 125 | 133 | 103 | 60 | 58.2524 | |
| ciseli-custom | INDEL | D6_15 | map_l100_m2_e0 | * | 54.3651 | 51.8939 | 57.0833 | 88.8786 | 137 | 127 | 137 | 103 | 60 | 58.2524 | |
| gduggal-snapplat | SNP | ti | map_l125_m0_e0 | * | 91.6685 | 88.4893 | 95.0846 | 83.9409 | 11293 | 1469 | 11297 | 584 | 340 | 58.2192 | |
| rpoplin-dv42 | SNP | * | map_l100_m2_e1 | * | 99.4091 | 99.2775 | 99.5411 | 65.1919 | 74197 | 540 | 74186 | 342 | 199 | 58.1871 | |
| ndellapenna-hhga | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 98.0218 | 97.3951 | 98.6566 | 81.2038 | 4038 | 108 | 4039 | 55 | 32 | 58.1818 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 81.8319 | 77.0675 | 87.2242 | 66.9862 | 1519 | 452 | 1502 | 220 | 128 | 58.1818 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 81.8319 | 77.0675 | 87.2242 | 66.9862 | 1519 | 452 | 1502 | 220 | 128 | 58.1818 | |
| eyeh-varpipe | INDEL | * | map_l125_m2_e1 | het | 96.7368 | 96.5199 | 96.9546 | 85.7560 | 1359 | 49 | 1751 | 55 | 32 | 58.1818 | |
| asubramanian-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 96.6230 | 97.5440 | 95.7192 | 65.8529 | 14258 | 359 | 15451 | 691 | 402 | 58.1766 | |
| ghariani-varprowl | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 82.1159 | 98.1982 | 70.5600 | 84.9325 | 436 | 8 | 441 | 184 | 107 | 58.1522 | |
| ciseli-custom | INDEL | * | map_l150_m2_e0 | het | 66.9093 | 62.8035 | 71.5895 | 93.6451 | 569 | 337 | 572 | 227 | 132 | 58.1498 | |
| cchapple-custom | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 99.1314 | 98.9416 | 99.3219 | 67.8823 | 6170 | 66 | 6298 | 43 | 25 | 58.1395 | |
| hfeng-pmm1 | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.2458 | 98.7161 | 99.7811 | 57.1497 | 19607 | 255 | 19600 | 43 | 25 | 58.1395 | |
| jpowers-varprowl | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 94.4879 | 99.7997 | 89.7129 | 85.3011 | 1495 | 3 | 1500 | 172 | 100 | 58.1395 | |
| anovak-vg | INDEL | I6_15 | map_l100_m2_e0 | * | 53.4759 | 49.1379 | 58.6538 | 81.9130 | 57 | 59 | 61 | 43 | 25 | 58.1395 | |
| gduggal-bwaplat | INDEL | I6_15 | HG002complexvar | * | 86.2963 | 77.2538 | 97.7362 | 64.0519 | 3702 | 1090 | 3713 | 86 | 50 | 58.1395 | |
| rpoplin-dv42 | SNP | tv | map_l150_m1_e0 | * | 98.9126 | 98.7903 | 99.0352 | 73.1204 | 10780 | 132 | 10778 | 105 | 61 | 58.0952 | |
| rpoplin-dv42 | SNP | tv | map_l150_m2_e0 | * | 98.9506 | 98.8287 | 99.0728 | 74.8529 | 11222 | 133 | 11220 | 105 | 61 | 58.0952 | |
| rpoplin-dv42 | SNP | tv | map_l150_m2_e1 | * | 98.9641 | 98.8437 | 99.0847 | 74.8658 | 11369 | 133 | 11367 | 105 | 61 | 58.0952 | |
| anovak-vg | INDEL | D1_5 | HG002complexvar | het | 92.0015 | 90.8693 | 93.1622 | 52.9821 | 18869 | 1896 | 19565 | 1436 | 834 | 58.0780 | |
| asubramanian-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.2746 | 98.1228 | 98.4270 | 77.7694 | 92676 | 1773 | 96110 | 1536 | 892 | 58.0729 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 96.2475 | 93.6213 | 99.0253 | 42.3352 | 6913 | 471 | 12598 | 124 | 72 | 58.0645 | |
| ndellapenna-hhga | SNP | * | HG002compoundhet | het | 98.0271 | 96.5510 | 99.5491 | 42.9549 | 13689 | 489 | 13687 | 62 | 36 | 58.0645 | |
| rpoplin-dv42 | INDEL | I1_5 | map_siren | * | 98.7675 | 98.5691 | 98.9667 | 80.4011 | 2962 | 43 | 2969 | 31 | 18 | 58.0645 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 92.7341 | 89.2791 | 96.4674 | 63.8560 | 13907 | 1670 | 13927 | 510 | 296 | 58.0392 | |
| gduggal-snapvard | INDEL | I16_PLUS | HG002complexvar | het | 3.1923 | 1.6541 | 45.5157 | 59.5648 | 11 | 654 | 203 | 243 | 141 | 58.0247 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.0351 | 96.4286 | 97.6493 | 76.4347 | 2079 | 77 | 2077 | 50 | 29 | 58.0000 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 95.3878 | 94.0484 | 96.7658 | 60.9497 | 1517 | 96 | 1496 | 50 | 29 | 58.0000 | |
| hfeng-pmm2 | INDEL | * | * | het | 99.3911 | 99.1521 | 99.6313 | 58.9414 | 192487 | 1646 | 192126 | 711 | 412 | 57.9466 | |
| jli-custom | INDEL | * | map_siren | homalt | 99.3607 | 99.4350 | 99.2865 | 79.8135 | 2640 | 15 | 2644 | 19 | 11 | 57.8947 | |
| hfeng-pmm3 | INDEL | D1_5 | HG002complexvar | het | 98.9670 | 98.0448 | 99.9068 | 54.1875 | 20359 | 406 | 20363 | 19 | 11 | 57.8947 | |
| gduggal-snapvard | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 1.1095 | 0.5618 | 44.1176 | 64.0212 | 1 | 177 | 30 | 38 | 22 | 57.8947 | |
| gduggal-snapvard | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 1.8131 | 0.9259 | 43.2836 | 64.1711 | 1 | 107 | 29 | 38 | 22 | 57.8947 | |
| ghariani-varprowl | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 68.4170 | 67.7419 | 69.1057 | 99.9232 | 84 | 40 | 85 | 38 | 22 | 57.8947 | |
| egarrison-hhga | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 96.9916 | 95.5731 | 98.4528 | 83.7652 | 1209 | 56 | 1209 | 19 | 11 | 57.8947 | |