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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
75401-75450 / 86044 show all | |||||||||||||||
| gduggal-snapplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 51.1782 | 35.9607 | 88.7235 | 60.7545 | 5046 | 8986 | 5067 | 644 | 550 | 85.4037 | |
| hfeng-pmm1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.3726 | 99.0232 | 99.7245 | 73.4687 | 5069 | 50 | 5067 | 14 | 4 | 28.5714 | |
| gduggal-snapvard | SNP | ti | HG002compoundhet | homalt | 89.4254 | 81.9989 | 98.3311 | 34.6481 | 6063 | 1331 | 5067 | 86 | 63 | 73.2558 | |
| asubramanian-gatk | SNP | tv | map_l125_m2_e1 | * | 46.6345 | 30.4256 | 99.8030 | 92.2720 | 5068 | 11589 | 5067 | 10 | 2 | 20.0000 | |
| ltrigg-rtg1 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 99.4112 | 98.9838 | 99.8424 | 34.1207 | 5065 | 52 | 5068 | 8 | 8 | 100.0000 | |
| cchapple-custom | INDEL | D16_PLUS | * | het | 96.8499 | 96.8344 | 96.8654 | 63.8824 | 3059 | 100 | 5068 | 164 | 133 | 81.0976 | |
| raldana-dualsentieon | SNP | * | map_l250_m2_e0 | het | 97.5099 | 97.6319 | 97.3881 | 89.3936 | 5071 | 123 | 5071 | 136 | 3 | 2.2059 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 96.9317 | 95.4084 | 98.5046 | 64.3470 | 5070 | 244 | 5072 | 77 | 69 | 89.6104 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 99.0240 | 99.1401 | 98.9082 | 42.6607 | 5073 | 44 | 5073 | 56 | 56 | 100.0000 | |
| jmaeng-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.3929 | 99.1600 | 99.6269 | 75.2923 | 5076 | 43 | 5074 | 19 | 13 | 68.4211 | |
| ltrigg-rtg1 | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.7403 | 96.1234 | 99.4126 | 61.0480 | 5108 | 206 | 5077 | 30 | 17 | 56.6667 | |
| jmaeng-gatk | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.2881 | 95.5213 | 99.1216 | 64.1698 | 5076 | 238 | 5078 | 45 | 35 | 77.7778 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.2477 | 99.2381 | 99.2572 | 75.1119 | 5080 | 39 | 5078 | 38 | 20 | 52.6316 | |
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.4518 | 99.2381 | 99.6663 | 75.2850 | 5080 | 39 | 5078 | 17 | 10 | 58.8235 | |
| gduggal-snapvard | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 52.6401 | 36.2653 | 95.9758 | 39.3144 | 3756 | 6601 | 5080 | 213 | 206 | 96.7136 | |
| ckim-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.4326 | 99.2967 | 99.5689 | 75.2558 | 5083 | 36 | 5081 | 22 | 10 | 45.4545 | |
| jli-custom | SNP | * | map_l250_m2_e1 | het | 97.7120 | 96.5426 | 98.9101 | 87.1957 | 5082 | 182 | 5082 | 56 | 24 | 42.8571 | |
| eyeh-varpipe | SNP | * | map_l250_m2_e1 | het | 98.4883 | 99.3731 | 97.6190 | 91.2048 | 5231 | 33 | 5084 | 124 | 8 | 6.4516 | |
| cchapple-custom | INDEL | D6_15 | HG002complexvar | * | 96.6422 | 95.3791 | 97.9391 | 52.4803 | 5057 | 245 | 5085 | 107 | 98 | 91.5888 | |
| ckim-dragen | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.5015 | 99.5702 | 99.4329 | 75.1639 | 5097 | 22 | 5085 | 29 | 11 | 37.9310 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 96.2898 | 93.2880 | 99.4913 | 26.4604 | 5073 | 365 | 5085 | 26 | 21 | 80.7692 | |
| cchapple-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 98.5950 | 99.6678 | 97.5451 | 34.2663 | 5100 | 17 | 5086 | 128 | 121 | 94.5312 | |
| qzeng-custom | SNP | * | map_l250_m2_e1 | * | 75.9076 | 64.2294 | 92.7764 | 95.4610 | 5130 | 2857 | 5086 | 396 | 330 | 83.3333 | |
| ghariani-varprowl | SNP | * | map_l250_m2_e0 | het | 94.4212 | 97.9207 | 91.1633 | 92.2470 | 5086 | 108 | 5086 | 493 | 83 | 16.8357 | |
| ckim-isaac | SNP | tv | segdup | het | 98.0147 | 96.1793 | 99.9214 | 89.5689 | 5085 | 202 | 5087 | 4 | 1 | 25.0000 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 99.2974 | 99.4333 | 99.1620 | 40.9075 | 5088 | 29 | 5088 | 43 | 42 | 97.6744 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 98.1100 | 99.2769 | 96.9703 | 51.0036 | 5080 | 37 | 5089 | 159 | 149 | 93.7107 | |
| jlack-gatk | SNP | * | map_l250_m2_e0 | het | 91.0733 | 98.0169 | 85.0484 | 94.0579 | 5091 | 103 | 5091 | 895 | 58 | 6.4805 | |
| eyeh-varpipe | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 83.2366 | 80.6994 | 85.9386 | 73.3453 | 4131 | 988 | 5091 | 833 | 775 | 93.0372 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 94.7163 | 99.4919 | 90.3781 | 51.0003 | 5091 | 26 | 5091 | 542 | 540 | 99.6310 | |
| gduggal-snapvard | SNP | tv | segdup | het | 97.6892 | 96.9926 | 98.3958 | 95.3896 | 5128 | 159 | 5091 | 83 | 12 | 14.4578 | |
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 99.2980 | 99.5114 | 99.0854 | 41.3691 | 5092 | 25 | 5092 | 47 | 47 | 100.0000 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 97.4266 | 99.5114 | 95.4273 | 42.4504 | 5092 | 25 | 5092 | 244 | 244 | 100.0000 | |
| ciseli-custom | SNP | * | map_l150_m0_e0 | het | 70.4472 | 64.1940 | 78.0503 | 88.1313 | 5097 | 2843 | 5092 | 1432 | 47 | 3.2821 | |
| ciseli-custom | SNP | * | map_l250_m2_e0 | * | 69.1818 | 64.6798 | 74.3575 | 92.1767 | 5100 | 2785 | 5092 | 1756 | 343 | 19.5330 | |
| rpoplin-dv42 | SNP | * | map_l250_m2_e0 | het | 98.1499 | 98.0554 | 98.2446 | 88.1117 | 5093 | 101 | 5093 | 91 | 56 | 61.5385 | |
| dgrover-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.5603 | 99.5507 | 99.5700 | 75.2360 | 5096 | 23 | 5094 | 22 | 10 | 45.4545 | |
| bgallagher-sentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.5214 | 99.5507 | 99.4922 | 74.9449 | 5096 | 23 | 5094 | 26 | 13 | 50.0000 | |
| astatham-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.5798 | 99.5507 | 99.6089 | 75.0780 | 5096 | 23 | 5094 | 20 | 10 | 50.0000 | |
| mlin-fermikit | SNP | tv | segdup | het | 97.5120 | 96.3685 | 98.6829 | 87.0738 | 5095 | 192 | 5095 | 68 | 1 | 1.4706 | |
| 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 | |
| ckim-vqsr | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.5490 | 95.8600 | 99.2985 | 63.8541 | 5094 | 220 | 5096 | 36 | 30 | 83.3333 | |
| gduggal-bwavard | SNP | * | map_l250_m2_e1 | het | 87.2283 | 97.7964 | 78.7214 | 93.0803 | 5148 | 116 | 5098 | 1378 | 35 | 2.5399 | |
| qzeng-custom | SNP | * | map_l150_m0_e0 | het | 75.9917 | 64.6851 | 92.0882 | 93.9068 | 5136 | 2804 | 5098 | 438 | 367 | 83.7900 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.6812 | 95.9164 | 99.5121 | 62.7887 | 5097 | 217 | 5099 | 25 | 19 | 76.0000 | |
| gduggal-bwavard | SNP | tv | segdup | het | 97.8517 | 97.1439 | 98.5698 | 95.5379 | 5136 | 151 | 5100 | 74 | 15 | 20.2703 | |
| ckim-gatk | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.5789 | 95.9353 | 99.2797 | 63.8316 | 5098 | 216 | 5100 | 37 | 30 | 81.0811 | |
| hfeng-pmm1 | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.6540 | 95.9541 | 99.4153 | 63.0411 | 5099 | 215 | 5101 | 30 | 22 | 73.3333 | |
| hfeng-pmm1 | SNP | * | map_l250_m2_e0 | het | 98.5614 | 98.2672 | 98.8573 | 88.7531 | 5104 | 90 | 5104 | 59 | 11 | 18.6441 | |