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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
12951-13000 / 86044 show all | |||||||||||||||
| jmaeng-gatk | INDEL | D1_5 | map_l125_m2_e1 | * | 96.2418 | 98.3578 | 94.2149 | 90.9091 | 1138 | 19 | 1140 | 70 | 6 | 8.5714 | |
| jmaeng-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 92.1277 | 99.0847 | 86.0835 | 48.4103 | 433 | 4 | 433 | 70 | 70 | 100.0000 | |
| jmaeng-gatk | SNP | ti | * | homalt | 99.6264 | 99.2642 | 99.9912 | 16.0789 | 797129 | 5909 | 797120 | 70 | 46 | 65.7143 | |
| anovak-vg | INDEL | I6_15 | segdup | * | 45.2111 | 40.5714 | 51.0490 | 89.3838 | 71 | 104 | 73 | 70 | 55 | 78.5714 | |
| astatham-gatk | INDEL | * | * | hetalt | 96.8001 | 94.0563 | 99.7088 | 58.1664 | 23737 | 1500 | 23968 | 70 | 69 | 98.5714 | |
| astatham-gatk | INDEL | * | map_l100_m2_e0 | * | 96.5801 | 95.1530 | 98.0507 | 86.7138 | 3514 | 179 | 3521 | 70 | 18 | 25.7143 | |
| astatham-gatk | INDEL | * | map_l100_m2_e1 | * | 96.5544 | 95.0745 | 98.0811 | 86.7793 | 3571 | 185 | 3578 | 70 | 18 | 25.7143 | |
| anovak-vg | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 9.6515 | 5.6250 | 33.9623 | 61.7329 | 27 | 453 | 36 | 70 | 34 | 48.5714 | |
| bgallagher-sentieon | INDEL | * | map_siren | het | 98.7628 | 99.0683 | 98.4592 | 83.3559 | 4466 | 42 | 4473 | 70 | 8 | 11.4286 | |
| bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.1344 | 98.2308 | 98.0381 | 71.7207 | 3498 | 63 | 3498 | 70 | 50 | 71.4286 | |
| astatham-gatk | INDEL | D16_PLUS | HG002compoundhet | het | 88.8320 | 99.5062 | 80.2260 | 58.8850 | 403 | 2 | 284 | 70 | 68 | 97.1429 | |
| astatham-gatk | INDEL | I16_PLUS | * | homalt | 97.6467 | 99.6797 | 95.6950 | 72.0858 | 1556 | 5 | 1556 | 70 | 68 | 97.1429 | |
| asubramanian-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 98.9717 | 99.0613 | 98.8823 | 57.7880 | 6015 | 57 | 6193 | 70 | 23 | 32.8571 | |
| asubramanian-gatk | INDEL | * | map_l100_m0_e0 | * | 91.6436 | 88.3557 | 95.1857 | 96.6934 | 1381 | 182 | 1384 | 70 | 8 | 11.4286 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | * | 90.2544 | 90.2041 | 90.3047 | 58.2659 | 663 | 72 | 652 | 70 | 64 | 91.4286 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 98.2279 | 99.3671 | 97.1146 | 56.0984 | 2355 | 15 | 2356 | 70 | 66 | 94.2857 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 88.5246 | 100.0000 | 79.4118 | 64.9485 | 153 | 0 | 270 | 70 | 69 | 98.5714 | |
| rpoplin-dv42 | INDEL | D6_15 | HG002complexvar | het | 97.7459 | 97.7564 | 97.7354 | 59.1947 | 3050 | 70 | 3021 | 70 | 62 | 88.5714 | |
| rpoplin-dv42 | INDEL | I6_15 | HG002complexvar | * | 96.7965 | 95.1586 | 98.4917 | 56.6586 | 4560 | 232 | 4571 | 70 | 64 | 91.4286 | |
| rpoplin-dv42 | INDEL | * | HG002complexvar | hetalt | 94.3915 | 91.0246 | 98.0170 | 68.2440 | 3367 | 332 | 3460 | 70 | 68 | 97.1429 | |
| rpoplin-dv42 | INDEL | D16_PLUS | HG002complexvar | * | 93.9813 | 92.4528 | 95.5612 | 63.5376 | 1519 | 124 | 1507 | 70 | 64 | 91.4286 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.2138 | 99.9488 | 96.5381 | 40.8253 | 1952 | 1 | 1952 | 70 | 69 | 98.5714 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 92.1109 | 98.8558 | 86.2275 | 47.5941 | 432 | 5 | 432 | 69 | 69 | 100.0000 | |
| rpoplin-dv42 | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 96.2570 | 93.3938 | 99.3014 | 31.9625 | 9783 | 692 | 9808 | 69 | 68 | 98.5507 | |
| rpoplin-dv42 | INDEL | I6_15 | * | homalt | 97.7056 | 96.5700 | 98.8683 | 48.6914 | 6025 | 214 | 6028 | 69 | 68 | 98.5507 | |
| hfeng-pmm1 | SNP | tv | map_siren | * | 99.7188 | 99.5885 | 99.8494 | 56.2301 | 45741 | 189 | 45734 | 69 | 22 | 31.8841 | |
| hfeng-pmm2 | INDEL | D1_5 | HG002compoundhet | homalt | 89.0601 | 99.3127 | 80.7263 | 78.1840 | 289 | 2 | 289 | 69 | 69 | 100.0000 | |
| hfeng-pmm2 | SNP | ti | map_l250_m2_e1 | het | 98.4165 | 98.9088 | 97.9292 | 90.8817 | 3263 | 36 | 3263 | 69 | 7 | 10.1449 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.1325 | 96.6975 | 99.6107 | 39.2966 | 17656 | 603 | 17657 | 69 | 63 | 91.3043 | |
| jlack-gatk | SNP | ti | HG002compoundhet | het | 99.4749 | 99.6739 | 99.2768 | 41.5881 | 9474 | 31 | 9472 | 69 | 16 | 23.1884 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 95.5076 | 97.4127 | 93.6755 | 70.3048 | 753 | 20 | 1022 | 69 | 54 | 78.2609 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 97.6743 | 98.7234 | 96.6472 | 38.6953 | 464 | 6 | 1989 | 69 | 66 | 95.6522 | |
| eyeh-varpipe | SNP | ti | lowcmp_SimpleRepeat_quadTR_51to200 | * | 59.9965 | 83.1683 | 46.9231 | 93.4110 | 84 | 17 | 61 | 69 | 13 | 18.8406 | |
| eyeh-varpipe | SNP | ti | map_l250_m2_e1 | het | 98.5825 | 99.2725 | 97.9021 | 91.2682 | 3275 | 24 | 3220 | 69 | 4 | 5.7971 | |
| eyeh-varpipe | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 73.1615 | 86.6667 | 63.2979 | 89.1767 | 143 | 22 | 119 | 69 | 11 | 15.9420 | |
| eyeh-varpipe | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | het | 98.2187 | 99.8597 | 96.6309 | 38.9931 | 2135 | 3 | 1979 | 69 | 6 | 8.6957 | |
| gduggal-bwavard | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 98.6965 | 98.0478 | 99.3539 | 59.8156 | 10698 | 213 | 10610 | 69 | 47 | 68.1159 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 92.3526 | 88.8889 | 96.0973 | 56.8254 | 1184 | 148 | 1699 | 69 | 59 | 85.5072 | |
| gduggal-bwavard | INDEL | D1_5 | map_l150_m0_e0 | * | 87.6716 | 96.8858 | 80.0578 | 92.5399 | 280 | 9 | 277 | 69 | 7 | 10.1449 | |
| gduggal-bwavard | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 78.0258 | 97.6378 | 64.9746 | 77.1991 | 124 | 3 | 128 | 69 | 47 | 68.1159 | |
| gduggal-bwavard | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 64.2663 | 78.7037 | 54.3046 | 76.0317 | 85 | 23 | 82 | 69 | 42 | 60.8696 | |
| dgrover-gatk | INDEL | I16_PLUS | * | homalt | 97.7415 | 99.8078 | 95.7591 | 72.2497 | 1558 | 3 | 1558 | 69 | 66 | 95.6522 | |
| ckim-vqsr | INDEL | I1_5 | HG002compoundhet | het | 94.8823 | 98.1176 | 91.8536 | 86.7262 | 834 | 16 | 778 | 69 | 67 | 97.1014 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 83.1362 | 81.1475 | 85.2248 | 77.0629 | 396 | 92 | 398 | 69 | 22 | 31.8841 | |
| ckim-isaac | SNP | * | * | homalt | 98.3805 | 96.8182 | 99.9940 | 14.4545 | 1142612 | 37550 | 1142668 | 69 | 50 | 72.4638 | |
| ckim-isaac | SNP | * | map_l125_m2_e1 | * | 73.7959 | 58.5590 | 99.7510 | 72.8548 | 27641 | 19561 | 27643 | 69 | 17 | 24.6377 | |
| ckim-isaac | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | * | 96.4572 | 94.0150 | 99.0295 | 31.3640 | 7006 | 446 | 7041 | 69 | 48 | 69.5652 | |
| ckim-vqsr | INDEL | D16_PLUS | HG002compoundhet | het | 88.8043 | 99.2593 | 80.3419 | 59.7015 | 402 | 3 | 282 | 69 | 67 | 97.1014 | |
| egarrison-hhga | SNP | * | map_l125_m1_e0 | het | 99.2263 | 98.7039 | 99.7544 | 69.9636 | 28024 | 368 | 28024 | 69 | 28 | 40.5797 | |
| egarrison-hhga | SNP | * | map_l150_m2_e1 | * | 99.3609 | 98.9413 | 99.7840 | 74.9205 | 31869 | 341 | 31869 | 69 | 32 | 46.3768 | |