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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
11401-11450 / 86044 show all | |||||||||||||||
| gduggal-bwafb | SNP | tv | map_l125_m0_e0 | het | 97.4938 | 98.1141 | 96.8813 | 79.0298 | 4318 | 83 | 4318 | 139 | 26 | 18.7050 | |
| egarrison-hhga | SNP | tv | map_l125_m0_e0 | het | 98.8440 | 98.1141 | 99.5849 | 74.9393 | 4318 | 83 | 4318 | 18 | 7 | 38.8889 | |
| ckim-isaac | SNP | tv | map_l100_m0_e0 | het | 74.7468 | 59.7757 | 99.7229 | 73.2042 | 4317 | 2905 | 4319 | 12 | 3 | 25.0000 | |
| mlin-fermikit | SNP | ti | map_l100_m0_e0 | homalt | 63.6297 | 55.5184 | 74.5166 | 48.8430 | 4316 | 3458 | 4316 | 1476 | 1404 | 95.1220 | |
| jpowers-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 52.1726 | 37.5740 | 85.3233 | 64.3826 | 4315 | 7169 | 4302 | 740 | 648 | 87.5676 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.2723 | 92.8126 | 100.0000 | 27.2105 | 4313 | 334 | 4363 | 0 | 0 | ||
| ckim-dragen | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.2607 | 92.7910 | 100.0000 | 26.5013 | 4312 | 335 | 4357 | 0 | 0 | ||
| ghariani-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 52.0817 | 37.5305 | 85.0613 | 64.9709 | 4310 | 7174 | 4299 | 755 | 639 | 84.6358 | |
| jli-custom | SNP | tv | map_l125_m0_e0 | het | 98.4127 | 97.9096 | 98.9210 | 71.8623 | 4309 | 92 | 4309 | 47 | 14 | 29.7872 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 94.8267 | 90.2557 | 99.8855 | 32.3046 | 4307 | 465 | 4360 | 5 | 4 | 80.0000 | |
| gduggal-bwavard | SNP | tv | func_cds | * | 99.0223 | 98.5358 | 99.5136 | 36.8583 | 4307 | 64 | 4296 | 21 | 9 | 42.8571 | |
| gduggal-snapvard | SNP | tv | func_cds | * | 98.8510 | 98.5129 | 99.1913 | 36.1464 | 4306 | 65 | 4293 | 35 | 10 | 28.5714 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 76.6168 | 62.5327 | 98.8894 | 32.4892 | 4306 | 2580 | 4007 | 45 | 40 | 88.8889 | |
| ckim-isaac | SNP | tv | func_cds | * | 99.2280 | 98.5129 | 99.9536 | 23.4678 | 4306 | 65 | 4306 | 2 | 0 | 0.0000 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 95.8836 | 92.6404 | 99.3621 | 26.9063 | 4305 | 342 | 4829 | 31 | 30 | 96.7742 | |
| asubramanian-gatk | SNP | * | map_l125_m1_e0 | homalt | 40.5846 | 25.4599 | 99.9768 | 87.4504 | 4304 | 12601 | 4304 | 1 | 0 | 0.0000 | |
| ckim-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.1468 | 92.6189 | 99.9541 | 23.6736 | 4304 | 343 | 4357 | 2 | 2 | 100.0000 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 85.2372 | 96.7836 | 76.1521 | 58.2609 | 4303 | 143 | 4825 | 1511 | 1481 | 98.0146 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.1236 | 92.5759 | 99.9541 | 23.6819 | 4302 | 345 | 4355 | 2 | 2 | 100.0000 | |
| qzeng-custom | SNP | * | map_l125_m0_e0 | homalt | 77.7882 | 64.0644 | 98.9949 | 72.2676 | 4300 | 2412 | 4235 | 43 | 42 | 97.6744 | |
| gduggal-bwavard | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 55.2412 | 96.6262 | 38.6762 | 52.9026 | 4296 | 150 | 4283 | 6791 | 6733 | 99.1459 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 76.5171 | 62.3875 | 98.9208 | 32.6004 | 4296 | 2590 | 4033 | 44 | 40 | 90.9091 | |
| gduggal-snapfb | SNP | ti | map_l250_m1_e0 | * | 94.3297 | 93.7323 | 94.9347 | 89.2465 | 4292 | 287 | 4292 | 229 | 122 | 53.2751 | |
| gduggal-bwaplat | SNP | tv | map_l100_m0_e0 | het | 74.3090 | 59.3741 | 99.2822 | 90.5912 | 4288 | 2934 | 4288 | 31 | 10 | 32.2581 | |
| gduggal-bwaplat | SNP | ti | map_l125_m0_e0 | het | 68.0749 | 51.8819 | 98.9622 | 92.4159 | 4287 | 3976 | 4291 | 45 | 14 | 31.1111 | |
| rpoplin-dv42 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 95.8100 | 92.2531 | 99.6523 | 26.1175 | 4287 | 360 | 4299 | 15 | 15 | 100.0000 | |
| cchapple-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 99.6741 | 99.7905 | 99.5579 | 54.7054 | 4286 | 9 | 4279 | 19 | 1 | 5.2632 | |
| astatham-gatk | SNP | * | map_l250_m2_e1 | het | 89.3080 | 81.4020 | 98.9151 | 92.3164 | 4285 | 979 | 4285 | 47 | 12 | 25.5319 | |
| rpoplin-dv42 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 99.7555 | 99.7439 | 99.7671 | 54.1386 | 4284 | 11 | 4284 | 10 | 2 | 20.0000 | |
| cchapple-custom | SNP | ti | map_l125_m0_e0 | homalt | 97.6182 | 95.3685 | 99.9767 | 63.8992 | 4283 | 208 | 4282 | 1 | 1 | 100.0000 | |
| eyeh-varpipe | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 95.9908 | 99.7206 | 92.5300 | 66.9362 | 4283 | 12 | 4162 | 336 | 9 | 2.6786 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 85.6750 | 96.3113 | 77.1544 | 58.1338 | 4282 | 164 | 4978 | 1474 | 1427 | 96.8114 | |
| jli-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 99.5467 | 99.6973 | 99.3965 | 52.0107 | 4282 | 13 | 4282 | 26 | 1 | 3.8462 | |
| gduggal-bwafb | INDEL | * | map_siren | het | 96.6142 | 94.9645 | 98.3223 | 79.9104 | 4281 | 227 | 4454 | 76 | 20 | 26.3158 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 94.5133 | 90.0694 | 99.4185 | 29.9723 | 4281 | 472 | 4274 | 25 | 22 | 88.0000 | |
| anovak-vg | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 71.6772 | 70.5040 | 72.8901 | 52.2851 | 4281 | 1791 | 4802 | 1786 | 1566 | 87.6820 | |
| gduggal-bwafb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.6955 | 99.6275 | 95.8371 | 67.9253 | 4279 | 16 | 4282 | 186 | 9 | 4.8387 | |
| ndellapenna-hhga | SNP | tv | map_l125_m0_e0 | het | 98.2879 | 97.1825 | 99.4189 | 73.8528 | 4277 | 124 | 4277 | 25 | 11 | 44.0000 | |
| egarrison-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 99.4422 | 99.5809 | 99.3038 | 58.0347 | 4277 | 18 | 4279 | 30 | 5 | 16.6667 | |
| eyeh-varpipe | INDEL | D1_5 | * | hetalt | 58.3169 | 41.7179 | 96.8535 | 76.3736 | 4274 | 5971 | 5356 | 174 | 162 | 93.1034 | |
| anovak-vg | SNP | tv | func_cds | * | 98.2741 | 97.7580 | 98.7957 | 36.4158 | 4273 | 98 | 4266 | 52 | 32 | 61.5385 | |
| jmaeng-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 95.7859 | 91.9518 | 99.9537 | 23.9402 | 4273 | 374 | 4322 | 2 | 2 | 100.0000 | |
| jpowers-varprowl | INDEL | I6_15 | * | homalt | 79.1239 | 68.4565 | 93.7294 | 42.5350 | 4271 | 1968 | 4275 | 286 | 264 | 92.3077 | |
| ltrigg-rtg1 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 98.3672 | 99.4179 | 97.3384 | 59.4908 | 4270 | 25 | 4352 | 119 | 1 | 0.8403 | |
| gduggal-bwaplat | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 83.3739 | 71.9097 | 99.1866 | 76.8457 | 4270 | 1668 | 4268 | 35 | 33 | 94.2857 | |
| ghariani-varprowl | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 96.7848 | 99.4179 | 94.2876 | 66.3675 | 4270 | 25 | 4275 | 259 | 18 | 6.9498 | |
| ndellapenna-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 99.2677 | 99.3946 | 99.1411 | 57.1258 | 4269 | 26 | 4271 | 37 | 6 | 16.2162 | |
| gduggal-snapfb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 85.0134 | 99.3714 | 74.2808 | 72.6746 | 4268 | 27 | 4312 | 1493 | 22 | 1.4735 | |
| bgallagher-sentieon | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 99.4872 | 99.3714 | 99.6033 | 48.0102 | 4268 | 27 | 4268 | 17 | 0 | 0.0000 | |
| jpowers-varprowl | INDEL | * | map_siren | het | 92.1013 | 94.6539 | 89.6827 | 84.2292 | 4267 | 241 | 4268 | 491 | 415 | 84.5214 | |