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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
76551-76600 / 86044 show all | |||||||||||||||
| qzeng-custom | SNP | tv | segdup | het | 97.9263 | 98.4679 | 97.3907 | 94.6360 | 5206 | 81 | 5188 | 139 | 6 | 4.3166 | |
| raldana-dualsentieon | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | het | 73.4719 | 85.9184 | 64.1753 | 76.0494 | 421 | 69 | 249 | 139 | 136 | 97.8417 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | * | 65.0860 | 56.7347 | 76.3203 | 57.3091 | 417 | 318 | 448 | 139 | 119 | 85.6115 | |
| gduggal-bwafb | SNP | tv | map_l125_m0_e0 | het | 97.4938 | 98.1141 | 96.8813 | 79.0298 | 4318 | 83 | 4318 | 139 | 26 | 18.7050 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 92.4416 | 88.7728 | 96.4267 | 49.8323 | 5266 | 666 | 3751 | 139 | 127 | 91.3669 | |
| gduggal-bwafb | SNP | * | map_l250_m2_e0 | het | 97.2051 | 97.0928 | 97.3176 | 90.2537 | 5043 | 151 | 5043 | 139 | 33 | 23.7410 | |
| gduggal-bwaplat | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 74.0031 | 64.7102 | 86.4125 | 82.4649 | 882 | 481 | 884 | 139 | 8 | 5.7554 | |
| gduggal-bwaplat | SNP | ti | segdup | het | 98.4906 | 98.1463 | 98.8374 | 94.7165 | 11807 | 223 | 11817 | 139 | 6 | 4.3166 | |
| eyeh-varpipe | INDEL | D1_5 | HG002complexvar | het | 98.4401 | 97.6258 | 99.2681 | 46.7116 | 20272 | 493 | 18853 | 139 | 98 | 70.5036 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 52.9384 | 36.4654 | 96.5577 | 59.1585 | 3388 | 5903 | 3899 | 139 | 129 | 92.8058 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 52.9384 | 36.4654 | 96.5577 | 59.1585 | 3388 | 5903 | 3899 | 139 | 129 | 92.8058 | |
| jpowers-varprowl | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 57.0116 | 54.1667 | 60.1719 | 83.5842 | 208 | 176 | 210 | 139 | 136 | 97.8417 | |
| jpowers-varprowl | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 65.1883 | 81.5920 | 54.2763 | 83.4962 | 164 | 37 | 165 | 139 | 136 | 97.8417 | |
| bgallagher-sentieon | SNP | * | map_l250_m2_e0 | het | 98.0598 | 98.7678 | 97.3619 | 90.6085 | 5130 | 64 | 5130 | 139 | 25 | 17.9856 | |
| asubramanian-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 96.2978 | 94.0048 | 98.7055 | 32.8581 | 9847 | 628 | 10599 | 139 | 132 | 94.9640 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.4170 | 92.5452 | 96.3660 | 61.9062 | 3687 | 297 | 3686 | 139 | 128 | 92.0863 | |
| astatham-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | het | 77.5406 | 92.6531 | 66.6667 | 80.5140 | 454 | 36 | 278 | 139 | 134 | 96.4029 | |
| anovak-vg | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 68.6189 | 80.5430 | 59.7701 | 87.2900 | 178 | 43 | 208 | 140 | 52 | 37.1429 | |
| bgallagher-sentieon | SNP | * | map_l250_m2_e1 | het | 98.0666 | 98.7652 | 97.3778 | 90.6744 | 5199 | 65 | 5199 | 140 | 25 | 17.8571 | |
| bgallagher-sentieon | INDEL | * | HG002complexvar | homalt | 99.7010 | 99.9186 | 99.4844 | 57.3638 | 27005 | 22 | 27015 | 140 | 135 | 96.4286 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.9950 | 99.9034 | 98.1030 | 36.7067 | 7240 | 7 | 7240 | 140 | 139 | 99.2857 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 96.7120 | 95.2896 | 98.1776 | 52.4952 | 5462 | 270 | 7542 | 140 | 133 | 95.0000 | |
| ndellapenna-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 96.6400 | 96.0539 | 97.2332 | 85.1791 | 4917 | 202 | 4920 | 140 | 101 | 72.1429 | |
| ndellapenna-hhga | SNP | * | map_l100_m2_e1 | * | 99.3413 | 98.8761 | 99.8109 | 63.7314 | 73897 | 840 | 73899 | 140 | 63 | 45.0000 | |
| qzeng-custom | INDEL | * | map_l125_m2_e1 | * | 82.9958 | 74.4270 | 93.7943 | 91.7220 | 1656 | 569 | 2116 | 140 | 47 | 33.5714 | |
| qzeng-custom | SNP | * | map_l100_m2_e1 | homalt | 87.9899 | 78.9574 | 99.3560 | 60.6459 | 21947 | 5849 | 21600 | 140 | 134 | 95.7143 | |
| mlin-fermikit | SNP | * | HG002complexvar | het | 98.1632 | 96.4217 | 99.9688 | 17.2653 | 448843 | 16657 | 448744 | 140 | 23 | 16.4286 | |
| mlin-fermikit | SNP | * | map_l250_m0_e0 | homalt | 49.5108 | 40.2226 | 64.3766 | 80.0000 | 253 | 376 | 253 | 140 | 131 | 93.5714 | |
| cchapple-custom | SNP | ti | map_l250_m1_e0 | * | 96.3982 | 95.8943 | 96.9074 | 89.5799 | 4391 | 188 | 4387 | 140 | 38 | 27.1429 | |
| ckim-dragen | SNP | ti | map_l250_m1_e0 | het | 96.2459 | 97.1361 | 95.3719 | 90.8281 | 2883 | 85 | 2885 | 140 | 10 | 7.1429 | |
| ckim-isaac | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 92.7880 | 87.7185 | 98.4794 | 33.6241 | 9085 | 1272 | 9067 | 140 | 97 | 69.2857 | |
| raldana-dualsentieon | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.0441 | 98.5197 | 99.5742 | 73.0561 | 32744 | 492 | 32737 | 140 | 116 | 82.8571 | |
| rpoplin-dv42 | SNP | tv | map_l100_m0_e0 | * | 98.7643 | 98.7911 | 98.7375 | 67.3276 | 10950 | 134 | 10949 | 140 | 63 | 45.0000 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 73.3614 | 64.8603 | 84.4271 | 38.2979 | 766 | 415 | 759 | 140 | 137 | 97.8571 | |
| gduggal-snapfb | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 70.8362 | 61.8574 | 82.8641 | 49.8157 | 373 | 230 | 677 | 140 | 133 | 95.0000 | |
| gduggal-snapvard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 95.0366 | 91.2990 | 99.0933 | 69.4457 | 15498 | 1477 | 15300 | 140 | 72 | 51.4286 | |
| gduggal-snapvard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 95.0366 | 91.2990 | 99.0933 | 69.4457 | 15498 | 1477 | 15300 | 140 | 72 | 51.4286 | |
| ghariani-varprowl | INDEL | D1_5 | map_l125_m2_e1 | het | 91.0832 | 98.8312 | 84.4617 | 91.0642 | 761 | 9 | 761 | 140 | 27 | 19.2857 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 22.5181 | 16.0393 | 37.7778 | 69.3878 | 98 | 513 | 85 | 140 | 43 | 30.7143 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 98.5527 | 99.8046 | 97.3318 | 50.7832 | 5107 | 10 | 5107 | 140 | 139 | 99.2857 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.6771 | 99.7888 | 97.5899 | 57.2270 | 5669 | 12 | 5669 | 140 | 139 | 99.2857 | |
| jmaeng-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 83.6527 | 80.4403 | 87.1324 | 45.1060 | 950 | 231 | 948 | 140 | 140 | 100.0000 | |
| jmaeng-gatk | SNP | ti | HG002complexvar | het | 99.7293 | 99.5044 | 99.9553 | 17.6005 | 313206 | 1560 | 313156 | 140 | 49 | 35.0000 | |
| ltrigg-rtg1 | SNP | tv | segdup | * | 98.9694 | 99.5663 | 98.3796 | 89.2053 | 8495 | 37 | 8500 | 140 | 20 | 14.2857 | |
| hfeng-pmm2 | SNP | ti | map_l125_m0_e0 | * | 99.1282 | 99.3496 | 98.9077 | 76.2142 | 12679 | 83 | 12677 | 140 | 17 | 12.1429 | |
| hfeng-pmm3 | SNP | * | map_l125_m2_e0 | het | 99.4247 | 99.3281 | 99.5214 | 72.2786 | 29121 | 197 | 29115 | 140 | 13 | 9.2857 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 93.8809 | 89.9476 | 98.1740 | 49.0700 | 7552 | 844 | 7527 | 140 | 92 | 65.7143 | |
| gduggal-bwafb | INDEL | I1_5 | HG002complexvar | homalt | 98.3809 | 97.8212 | 98.9471 | 49.0711 | 13155 | 293 | 13156 | 140 | 134 | 95.7143 | |
| gduggal-bwafb | SNP | * | map_l250_m1_e0 | * | 97.6861 | 97.3276 | 98.0471 | 89.3479 | 7029 | 193 | 7029 | 140 | 38 | 27.1429 | |
| gduggal-bwaplat | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 88.3800 | 79.7888 | 99.0444 | 59.7268 | 14508 | 3675 | 14511 | 140 | 39 | 27.8571 | |