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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
81501-81550 / 86044 show all | |||||||||||||||
| jli-custom | INDEL | I6_15 | * | * | 97.9633 | 96.9786 | 98.9683 | 47.9648 | 24073 | 750 | 24077 | 251 | 222 | 88.4462 | |
| ghariani-varprowl | SNP | * | map_l150_m1_e0 | * | 97.5510 | 98.4482 | 96.6701 | 79.2964 | 30134 | 475 | 30134 | 1038 | 222 | 21.3873 | |
| egarrison-hhga | INDEL | I6_15 | * | homalt | 96.9232 | 97.9324 | 95.9347 | 48.1653 | 6110 | 129 | 6112 | 259 | 222 | 85.7143 | |
| ckim-vqsr | INDEL | * | HG002complexvar | * | 99.2578 | 98.8640 | 99.6548 | 58.2159 | 76064 | 874 | 75924 | 263 | 222 | 84.4106 | |
| astatham-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.7180 | 99.3371 | 98.1066 | 65.6768 | 12438 | 83 | 12280 | 237 | 222 | 93.6709 | |
| qzeng-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 74.7354 | 78.9833 | 70.9211 | 58.2978 | 1041 | 277 | 1178 | 483 | 222 | 45.9627 | |
| ndellapenna-hhga | SNP | ti | HG002complexvar | * | 99.8069 | 99.6755 | 99.9387 | 17.4775 | 506786 | 1650 | 506808 | 311 | 223 | 71.7042 | |
| egarrison-hhga | SNP | * | HG002complexvar | * | 99.8252 | 99.7002 | 99.9506 | 18.9844 | 752119 | 2262 | 752170 | 372 | 223 | 59.9462 | |
| jmaeng-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.6853 | 98.9657 | 98.4065 | 63.1662 | 15597 | 163 | 15439 | 250 | 223 | 89.2000 | |
| jpowers-varprowl | INDEL | * | segdup | * | 89.1593 | 88.3803 | 89.9522 | 94.2165 | 2259 | 297 | 2256 | 252 | 223 | 88.4921 | |
| hfeng-pmm2 | INDEL | I6_15 | * | homalt | 98.0364 | 99.6314 | 96.4918 | 51.1007 | 6216 | 23 | 6216 | 226 | 223 | 98.6726 | |
| ghariani-varprowl | SNP | * | map_l150_m2_e0 | * | 97.6045 | 98.4962 | 96.7287 | 80.6842 | 31373 | 479 | 31373 | 1061 | 223 | 21.0179 | |
| hfeng-pmm1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 97.2261 | 96.1390 | 98.3380 | 67.3449 | 17131 | 688 | 16745 | 283 | 223 | 78.7986 | |
| ghariani-varprowl | INDEL | * | segdup | * | 89.4068 | 90.3756 | 88.4586 | 97.2748 | 2310 | 246 | 2307 | 301 | 223 | 74.0864 | |
| gduggal-snapvard | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 58.2286 | 59.3301 | 57.1672 | 32.0973 | 248 | 170 | 335 | 251 | 223 | 88.8446 | |
| gduggal-snapvard | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | het | 66.7314 | 81.9672 | 56.2718 | 32.0710 | 100 | 22 | 323 | 251 | 223 | 88.8446 | |
| gduggal-snapfb | SNP | tv | map_l100_m1_e0 | het | 97.0635 | 98.4108 | 95.7526 | 68.5715 | 15172 | 245 | 15172 | 673 | 223 | 33.1352 | |
| gduggal-snapfb | SNP | tv | map_l100_m2_e0 | het | 97.1053 | 98.4471 | 95.7997 | 70.6844 | 15532 | 245 | 15532 | 681 | 223 | 32.7460 | |
| gduggal-snapfb | SNP | tv | map_l100_m2_e1 | het | 97.1282 | 98.4628 | 95.8293 | 70.7561 | 15693 | 245 | 15693 | 683 | 223 | 32.6501 | |
| anovak-vg | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 94.8271 | 96.9609 | 92.7851 | 60.5360 | 3350 | 105 | 3498 | 272 | 223 | 81.9853 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 74.3243 | 87.7660 | 64.4531 | 60.5344 | 495 | 69 | 495 | 273 | 223 | 81.6850 | |
| ciseli-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 87.9595 | 98.3397 | 79.5614 | 83.1943 | 3850 | 65 | 3846 | 988 | 223 | 22.5709 | |
| cchapple-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.4367 | 96.0623 | 98.8510 | 34.0969 | 19785 | 811 | 20562 | 239 | 223 | 93.3054 | |
| hfeng-pmm2 | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.2602 | 91.5616 | 97.1227 | 66.9273 | 9223 | 850 | 9080 | 269 | 224 | 83.2714 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 75.3208 | 65.0467 | 89.4493 | 64.1933 | 2088 | 1122 | 2128 | 251 | 224 | 89.2430 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 90.5655 | 87.6892 | 93.6369 | 59.5069 | 3419 | 480 | 3414 | 232 | 224 | 96.5517 | |
| gduggal-bwavard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 92.2695 | 91.8075 | 92.7362 | 81.6429 | 17975 | 1604 | 17848 | 1398 | 224 | 16.0229 | |
| gduggal-bwavard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 92.2695 | 91.8075 | 92.7362 | 81.6429 | 17975 | 1604 | 17848 | 1398 | 224 | 16.0229 | |
| gduggal-bwavard | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | * | 12.5633 | 8.8953 | 21.3793 | 49.9136 | 62 | 635 | 62 | 228 | 224 | 98.2456 | |
| gduggal-bwavard | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 29.1765 | 45.9259 | 21.3793 | 49.5652 | 62 | 73 | 62 | 228 | 224 | 98.2456 | |
| anovak-vg | INDEL | * | map_l150_m1_e0 | * | 72.5622 | 74.5142 | 70.7099 | 89.9578 | 997 | 341 | 1026 | 425 | 224 | 52.7059 | |
| ghariani-varprowl | SNP | * | map_l150_m2_e1 | * | 97.6142 | 98.5067 | 96.7377 | 80.7467 | 31729 | 481 | 31729 | 1070 | 224 | 20.9346 | |
| gduggal-snapvard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 86.9733 | 91.1887 | 83.1303 | 79.6742 | 28398 | 2744 | 28182 | 5719 | 224 | 3.9168 | |
| gduggal-snapvard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 86.9733 | 91.1887 | 83.1303 | 79.6742 | 28398 | 2744 | 28182 | 5719 | 224 | 3.9168 | |
| gduggal-snapvard | SNP | ti | map_l125_m1_e0 | * | 93.7547 | 96.2264 | 91.4068 | 77.7724 | 28228 | 1107 | 27965 | 2629 | 225 | 8.5584 | |
| gduggal-snapvard | SNP | ti | map_l125_m2_e0 | * | 93.8841 | 96.2555 | 91.6267 | 79.1557 | 29125 | 1133 | 28856 | 2637 | 225 | 8.5324 | |
| gduggal-snapplat | INDEL | * | HG002complexvar | hetalt | 48.8074 | 34.6851 | 82.3281 | 84.4012 | 1283 | 2416 | 1365 | 293 | 225 | 76.7918 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 70.1659 | 88.4506 | 58.1458 | 66.8417 | 2175 | 284 | 2791 | 2009 | 225 | 11.1996 | |
| gduggal-snapplat | SNP | ti | map_l150_m0_e0 | * | 90.2459 | 86.2613 | 94.6165 | 87.8341 | 6781 | 1080 | 6784 | 386 | 225 | 58.2902 | |
| anovak-vg | INDEL | I16_PLUS | HG002complexvar | * | 33.1975 | 24.5225 | 51.3699 | 42.4631 | 321 | 988 | 300 | 284 | 225 | 79.2254 | |
| anovak-vg | SNP | ti | map_siren | homalt | 94.0329 | 89.3343 | 99.2531 | 48.3941 | 33872 | 4044 | 33489 | 252 | 225 | 89.2857 | |
| rpoplin-dv42 | SNP | * | map_siren | * | 99.6224 | 99.5097 | 99.7354 | 54.5067 | 145511 | 717 | 145497 | 386 | 225 | 58.2902 | |
| eyeh-varpipe | INDEL | I1_5 | HG002compoundhet | het | 74.0633 | 83.6471 | 66.4499 | 67.5390 | 711 | 139 | 511 | 258 | 225 | 87.2093 | |
| gduggal-bwafb | SNP | * | map_siren | * | 99.2387 | 99.3893 | 99.0885 | 58.6242 | 145335 | 893 | 145339 | 1337 | 225 | 16.8287 | |
| eyeh-varpipe | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 53.8085 | 55.7377 | 52.0085 | 38.7306 | 68 | 54 | 246 | 227 | 226 | 99.5595 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 86.9083 | 88.9474 | 84.9606 | 72.8067 | 1183 | 147 | 1401 | 248 | 226 | 91.1290 | |
| ckim-gatk | INDEL | * | HG002complexvar | * | 99.3276 | 99.0226 | 99.6345 | 58.1713 | 76186 | 752 | 76048 | 279 | 226 | 81.0036 | |
| cchapple-custom | SNP | ti | map_l125_m1_e0 | het | 96.3594 | 97.1203 | 95.6103 | 76.7136 | 17740 | 526 | 17751 | 815 | 226 | 27.7301 | |
| gduggal-snapvard | SNP | ti | map_l125_m2_e1 | * | 93.9227 | 96.2838 | 91.6745 | 79.2018 | 29433 | 1136 | 29158 | 2648 | 226 | 8.5347 | |
| gduggal-snapplat | INDEL | D6_15 | HG002compoundhet | homalt | 5.2905 | 29.1667 | 2.9091 | 54.3189 | 7 | 17 | 8 | 267 | 226 | 84.6442 | |