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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
9151-9200 / 86044 show all | |||||||||||||||
| ndellapenna-hhga | INDEL | D16_PLUS | HG002complexvar | * | 84.9902 | 80.5843 | 89.9058 | 63.0348 | 1324 | 319 | 1336 | 150 | 106 | 70.6667 | |
| rpoplin-dv42 | INDEL | I16_PLUS | * | * | 94.2741 | 91.2655 | 97.4879 | 59.7696 | 5820 | 557 | 5821 | 150 | 140 | 93.3333 | |
| asubramanian-gatk | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | het | 97.8791 | 98.9123 | 96.8672 | 42.4242 | 4638 | 51 | 4638 | 150 | 2 | 1.3333 | |
| anovak-vg | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 96.3287 | 96.4131 | 96.2444 | 58.5642 | 3790 | 141 | 3844 | 150 | 63 | 42.0000 | |
| anovak-vg | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 97.8222 | 97.8503 | 97.7942 | 34.8099 | 6600 | 145 | 6606 | 149 | 125 | 83.8926 | |
| anovak-vg | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 96.8834 | 96.9671 | 96.7998 | 38.7932 | 4476 | 140 | 4507 | 149 | 76 | 51.0067 | |
| bgallagher-sentieon | SNP | * | map_l250_m2_e1 | * | 98.4903 | 98.8356 | 98.1475 | 89.5400 | 7894 | 93 | 7894 | 149 | 32 | 21.4765 | |
| bgallagher-sentieon | SNP | tv | map_l150_m1_e0 | het | 98.5918 | 99.3090 | 97.8850 | 78.8267 | 6898 | 48 | 6896 | 149 | 20 | 13.4228 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 96.5828 | 95.1281 | 98.0826 | 45.6725 | 5643 | 289 | 7622 | 149 | 142 | 95.3020 | |
| jlack-gatk | INDEL | * | map_l150_m1_e0 | het | 91.0230 | 98.0117 | 84.9647 | 93.0437 | 838 | 17 | 842 | 149 | 6 | 4.0269 | |
| hfeng-pmm3 | SNP | * | map_l150_m1_e0 | * | 99.4475 | 99.3825 | 99.5125 | 74.0748 | 30420 | 189 | 30414 | 149 | 23 | 15.4362 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 85.5631 | 82.9787 | 88.3137 | 74.1798 | 1131 | 232 | 1126 | 149 | 144 | 96.6443 | |
| jmaeng-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 96.8289 | 96.6593 | 96.9990 | 75.1800 | 4832 | 167 | 4816 | 149 | 119 | 79.8658 | |
| jmaeng-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 96.8289 | 96.6593 | 96.9990 | 75.1800 | 4832 | 167 | 4816 | 149 | 119 | 79.8658 | |
| ltrigg-rtg2 | INDEL | * | HG002compoundhet | homalt | 87.5156 | 94.1691 | 81.7402 | 67.9371 | 646 | 40 | 667 | 149 | 147 | 98.6577 | |
| jmaeng-gatk | SNP | tv | map_l125_m0_e0 | * | 75.4933 | 61.9967 | 96.5015 | 90.4918 | 4111 | 2520 | 4110 | 149 | 7 | 4.6980 | |
| gduggal-snapplat | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 26.6667 | 33.8710 | 21.9895 | 96.6397 | 42 | 82 | 42 | 149 | 5 | 3.3557 | |
| gduggal-snapplat | INDEL | D1_5 | map_l100_m2_e1 | het | 85.1359 | 81.6246 | 88.9630 | 91.9002 | 1035 | 233 | 1201 | 149 | 28 | 18.7919 | |
| ghariani-varprowl | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 95.0613 | 99.1139 | 91.3271 | 69.3870 | 1566 | 14 | 1569 | 149 | 0 | 0.0000 | |
| gduggal-snapfb | INDEL | * | map_l100_m2_e0 | * | 93.4957 | 91.3079 | 95.7910 | 84.8783 | 3372 | 321 | 3391 | 149 | 39 | 26.1745 | |
| gduggal-bwafb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 82.7375 | 72.6354 | 96.1036 | 54.2365 | 1582 | 596 | 3675 | 149 | 111 | 74.4966 | |
| eyeh-varpipe | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 62.8380 | 55.5936 | 72.2533 | 62.8887 | 487 | 389 | 388 | 149 | 145 | 97.3154 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 61.3581 | 44.8472 | 97.1096 | 76.3054 | 4169 | 5127 | 5006 | 149 | 142 | 95.3020 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 90.7286 | 91.6605 | 89.8154 | 74.1565 | 1242 | 113 | 1314 | 149 | 130 | 87.2483 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 81.0289 | 75.8175 | 87.0096 | 52.5248 | 997 | 318 | 998 | 149 | 131 | 87.9195 | |
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 93.5626 | 98.9848 | 88.7036 | 60.4379 | 1170 | 12 | 1170 | 149 | 147 | 98.6577 | |
| dgrover-gatk | SNP | ti | map_l150_m2_e1 | * | 99.2396 | 99.1990 | 99.2803 | 78.3146 | 20557 | 166 | 20553 | 149 | 36 | 24.1611 | |
| dgrover-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 94.5951 | 96.6483 | 92.6274 | 77.7912 | 2105 | 73 | 1872 | 149 | 135 | 90.6040 | |
| rpoplin-dv42 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 99.6169 | 99.5602 | 99.6736 | 72.0020 | 45501 | 201 | 45497 | 149 | 51 | 34.2282 | |
| rpoplin-dv42 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 99.6169 | 99.5602 | 99.6736 | 72.0020 | 45501 | 201 | 45497 | 149 | 51 | 34.2282 | |
| cchapple-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 95.6652 | 95.1622 | 96.1736 | 68.5790 | 1731 | 88 | 3745 | 149 | 130 | 87.2483 | |
| cchapple-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 95.6652 | 95.1622 | 96.1736 | 68.5790 | 1731 | 88 | 3745 | 149 | 130 | 87.2483 | |
| ckim-gatk | SNP | tv | segdup | het | 98.3440 | 99.4704 | 97.2428 | 95.8012 | 5259 | 28 | 5255 | 149 | 0 | 0.0000 | |
| ckim-dragen | SNP | ti | map_l250_m2_e0 | het | 96.3935 | 97.2956 | 95.5080 | 91.3622 | 3166 | 88 | 3168 | 149 | 10 | 6.7114 | |
| ciseli-custom | SNP | tv | map_l250_m0_e0 | het | 59.1512 | 52.9720 | 66.9623 | 96.1499 | 303 | 269 | 302 | 149 | 7 | 4.6980 | |
| ckim-dragen | SNP | ti | map_l250_m1_e0 | * | 97.2516 | 97.7288 | 96.7791 | 88.9718 | 4475 | 104 | 4477 | 149 | 18 | 12.0805 | |
| qzeng-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 69.4565 | 77.0732 | 63.2099 | 78.1317 | 158 | 47 | 256 | 149 | 117 | 78.5235 | |
| qzeng-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 69.4565 | 77.0732 | 63.2099 | 78.1317 | 158 | 47 | 256 | 149 | 117 | 78.5235 | |
| mlin-fermikit | SNP | ti | map_l125_m2_e0 | het | 62.0977 | 45.3857 | 98.2903 | 64.2784 | 8567 | 10309 | 8566 | 149 | 7 | 4.6980 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 81.7913 | 85.3474 | 78.5196 | 66.0925 | 565 | 97 | 541 | 148 | 141 | 95.2703 | |
| ndellapenna-hhga | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.7167 | 98.4558 | 98.9789 | 74.5335 | 14346 | 225 | 14346 | 148 | 46 | 31.0811 | |
| ndellapenna-hhga | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.7167 | 98.4558 | 98.9789 | 74.5335 | 14346 | 225 | 14346 | 148 | 46 | 31.0811 | |
| mlin-fermikit | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 92.1665 | 91.3265 | 93.0222 | 72.9912 | 1969 | 187 | 1973 | 148 | 100 | 67.5676 | |
| mlin-fermikit | INDEL | * | map_l100_m0_e0 | homalt | 68.0723 | 66.6012 | 69.6099 | 79.4167 | 339 | 170 | 339 | 148 | 123 | 83.1081 | |
| mlin-fermikit | INDEL | D16_PLUS | HG002complexvar | * | 88.7656 | 86.9142 | 90.6977 | 68.5511 | 1428 | 215 | 1443 | 148 | 132 | 89.1892 | |
| gduggal-bwavard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 75.9578 | 85.7513 | 68.1720 | 92.2629 | 331 | 55 | 317 | 148 | 24 | 16.2162 | |
| gduggal-bwaplat | INDEL | I6_15 | * | hetalt | 85.2525 | 75.5818 | 97.7610 | 47.7759 | 6463 | 2088 | 6462 | 148 | 138 | 93.2432 | |
| eyeh-varpipe | SNP | ti | map_l150_m0_e0 | * | 98.7920 | 99.4784 | 98.1149 | 82.5537 | 7820 | 41 | 7703 | 148 | 7 | 4.7297 | |
| jmaeng-gatk | SNP | tv | map_l125_m0_e0 | het | 78.5795 | 66.8939 | 95.2119 | 92.0071 | 2944 | 1457 | 2943 | 148 | 6 | 4.0541 | |
| jpowers-varprowl | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 79.9744 | 90.9326 | 71.3733 | 92.8433 | 351 | 35 | 369 | 148 | 33 | 22.2973 | |