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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
11701-11750 / 86044 show all | |||||||||||||||
| gduggal-snapplat | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 40.4600 | 27.3210 | 77.9449 | 70.7692 | 309 | 822 | 311 | 88 | 69 | 78.4091 | |
| gduggal-bwaplat | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 61.6323 | 46.5246 | 91.2698 | 88.3076 | 917 | 1054 | 920 | 88 | 9 | 10.2273 | |
| gduggal-bwaplat | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 61.6323 | 46.5246 | 91.2698 | 88.3076 | 917 | 1054 | 920 | 88 | 9 | 10.2273 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | * | 75.9280 | 67.6190 | 86.5649 | 44.3027 | 497 | 238 | 567 | 88 | 88 | 100.0000 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | * | 70.1122 | 60.5452 | 83.2700 | 54.5769 | 422 | 275 | 438 | 88 | 86 | 97.7273 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 89.7585 | 88.5572 | 90.9928 | 62.2488 | 890 | 115 | 889 | 88 | 82 | 93.1818 | |
| eyeh-varpipe | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 69.9877 | 92.1053 | 56.4356 | 92.2038 | 140 | 12 | 114 | 88 | 4 | 4.5455 | |
| eyeh-varpipe | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.7434 | 99.1886 | 98.3021 | 75.3952 | 5379 | 44 | 5095 | 88 | 22 | 25.0000 | |
| eyeh-varpipe | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.7434 | 99.1886 | 98.3021 | 75.3952 | 5379 | 44 | 5095 | 88 | 22 | 25.0000 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 56.8463 | 56.2189 | 57.4879 | 72.4734 | 113 | 88 | 119 | 88 | 85 | 96.5909 | |
| ckim-dragen | SNP | tv | map_l250_m2_e1 | * | 97.2113 | 97.4280 | 96.9956 | 89.9894 | 2841 | 75 | 2841 | 88 | 12 | 13.6364 | |
| ckim-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.3059 | 99.0585 | 99.5546 | 59.8847 | 19675 | 187 | 19668 | 88 | 46 | 52.2727 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 99.0407 | 99.9158 | 98.1807 | 50.4457 | 4749 | 4 | 4749 | 88 | 87 | 98.8636 | |
| cchapple-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 93.9600 | 91.6530 | 96.3860 | 42.0652 | 560 | 51 | 2347 | 88 | 80 | 90.9091 | |
| ckim-dragen | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.6778 | 99.6209 | 99.7347 | 74.4322 | 33110 | 126 | 33088 | 88 | 54 | 61.3636 | |
| ckim-dragen | INDEL | I16_PLUS | * | homalt | 97.0983 | 99.6797 | 94.6472 | 70.1850 | 1556 | 5 | 1556 | 88 | 85 | 96.5909 | |
| hfeng-pmm1 | SNP | * | segdup | * | 99.7400 | 99.7934 | 99.6867 | 89.3409 | 28009 | 58 | 28003 | 88 | 11 | 12.5000 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.5311 | 96.0668 | 99.0408 | 42.6732 | 9086 | 372 | 9086 | 88 | 81 | 92.0455 | |
| hfeng-pmm2 | INDEL | I16_PLUS | * | * | 97.5355 | 96.5031 | 98.5902 | 69.5601 | 6154 | 223 | 6154 | 88 | 61 | 69.3182 | |
| jlack-gatk | INDEL | D1_5 | HG002complexvar | het | 99.5570 | 99.5377 | 99.5763 | 55.9428 | 20669 | 96 | 20681 | 88 | 29 | 32.9545 | |
| mlin-fermikit | SNP | ti | map_l100_m0_e0 | het | 57.7466 | 40.8496 | 98.4828 | 55.5044 | 5712 | 8271 | 5712 | 88 | 4 | 4.5455 | |
| qzeng-custom | INDEL | * | segdup | het | 96.2903 | 97.8854 | 94.7463 | 95.5784 | 1435 | 31 | 1587 | 88 | 19 | 21.5909 | |
| mlin-fermikit | INDEL | D16_PLUS | HG002complexvar | homalt | 84.2050 | 94.4637 | 75.9563 | 78.1493 | 273 | 16 | 278 | 88 | 85 | 96.5909 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 65.2356 | 95.9184 | 49.4253 | 67.9558 | 47 | 2 | 86 | 88 | 8 | 9.0909 | |
| qzeng-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 98.6961 | 99.6184 | 97.7906 | 64.7616 | 3916 | 15 | 3895 | 88 | 3 | 3.4091 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.3482 | 99.9034 | 98.7991 | 36.8548 | 7240 | 7 | 7240 | 88 | 87 | 98.8636 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 99.0301 | 99.8948 | 98.1803 | 50.4508 | 4748 | 5 | 4748 | 88 | 87 | 98.8636 | |
| egarrison-hhga | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 77.4016 | 63.6945 | 98.6259 | 40.8078 | 6672 | 3803 | 6316 | 88 | 82 | 93.1818 | |
| egarrison-hhga | SNP | * | map_l125_m2_e1 | * | 99.4493 | 99.0890 | 99.8122 | 70.5609 | 46772 | 430 | 46772 | 88 | 41 | 46.5909 | |
| egarrison-hhga | SNP | tv | * | homalt | 99.9252 | 99.8738 | 99.9766 | 20.9039 | 376647 | 476 | 376656 | 88 | 60 | 68.1818 | |
| eyeh-varpipe | INDEL | * | map_l125_m1_e0 | * | 96.4644 | 96.0133 | 96.9198 | 94.1307 | 2023 | 84 | 2769 | 88 | 62 | 70.4545 | |
| astatham-gatk | SNP | * | map_l100_m2_e1 | het | 86.9224 | 77.0139 | 99.7569 | 75.4083 | 36118 | 10780 | 36107 | 88 | 33 | 37.5000 | |
| asubramanian-gatk | INDEL | C1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 0.0000 | 0.0000 | 74.2690 | 0 | 1 | 0 | 88 | 0 | 0.0000 | ||
| asubramanian-gatk | INDEL | D1_5 | HG002complexvar | * | 99.2090 | 98.6948 | 99.7287 | 58.8075 | 32288 | 427 | 32347 | 88 | 75 | 85.2273 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 96.9370 | 94.9441 | 99.0153 | 65.4795 | 8826 | 470 | 8849 | 88 | 83 | 94.3182 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.1607 | 93.4776 | 99.0024 | 33.2299 | 8685 | 606 | 8733 | 88 | 82 | 93.1818 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.1607 | 93.4776 | 99.0024 | 33.2299 | 8685 | 606 | 8733 | 88 | 82 | 93.1818 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 87.7317 | 98.1043 | 79.3427 | 59.5442 | 207 | 4 | 338 | 88 | 87 | 98.8636 | |
| bgallagher-sentieon | SNP | ti | HG002complexvar | het | 99.9477 | 99.9234 | 99.9720 | 16.9632 | 314525 | 241 | 314471 | 88 | 29 | 32.9545 | |
| astatham-gatk | INDEL | * | HG002complexvar | het | 99.5588 | 99.3119 | 99.8070 | 57.7885 | 45894 | 318 | 45516 | 88 | 55 | 62.5000 | |
| anovak-vg | INDEL | * | map_l250_m2_e1 | het | 65.6155 | 68.2464 | 63.1799 | 96.7945 | 144 | 67 | 151 | 88 | 29 | 32.9545 | |
| ltrigg-rtg1 | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.8475 | 97.9811 | 99.7293 | 70.4300 | 32565 | 671 | 32421 | 88 | 29 | 32.9545 | |
| jmaeng-gatk | SNP | tv | HG002complexvar | * | 99.5035 | 99.0473 | 99.9639 | 22.5835 | 243807 | 2345 | 243715 | 88 | 31 | 35.2273 | |
| jmaeng-gatk | SNP | tv | map_l150_m0_e0 | * | 71.1604 | 56.3967 | 96.3949 | 93.3607 | 2354 | 1820 | 2353 | 88 | 6 | 6.8182 | |
| jpowers-varprowl | INDEL | D1_5 | map_l100_m2_e0 | het | 94.5055 | 95.8599 | 93.1889 | 86.1907 | 1204 | 52 | 1204 | 88 | 61 | 69.3182 | |
| jmaeng-gatk | INDEL | * | map_l150_m1_e0 | * | 95.7315 | 97.8326 | 93.7188 | 92.7638 | 1309 | 29 | 1313 | 88 | 9 | 10.2273 | |
| jmaeng-gatk | INDEL | * | map_l150_m2_e1 | het | 94.5416 | 98.0519 | 91.2738 | 94.1930 | 906 | 18 | 910 | 87 | 6 | 6.8966 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.0155 | 96.3678 | 99.7204 | 49.6879 | 30830 | 1162 | 31028 | 87 | 75 | 86.2069 | |
| ltrigg-rtg1 | SNP | * | map_l125_m2_e1 | het | 98.7345 | 97.7868 | 99.7007 | 62.3395 | 28984 | 656 | 28985 | 87 | 12 | 13.7931 | |
| jmaeng-gatk | SNP | tv | map_l150_m0_e0 | het | 74.0589 | 60.6050 | 95.1907 | 94.3590 | 1723 | 1120 | 1722 | 87 | 5 | 5.7471 | |