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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
55001-55050 / 86044 show all | |||||||||||||||
| gduggal-bwafb | INDEL | I1_5 | map_l250_m2_e0 | het | 92.8000 | 87.8788 | 98.3051 | 96.3286 | 58 | 8 | 58 | 1 | 0 | 0.0000 | |
| gduggal-bwafb | INDEL | I1_5 | map_l250_m2_e1 | het | 92.8000 | 87.8788 | 98.3051 | 96.4393 | 58 | 8 | 58 | 1 | 0 | 0.0000 | |
| jlack-gatk | INDEL | D6_15 | map_l100_m1_e0 | * | 92.8030 | 94.9612 | 90.7407 | 88.2660 | 245 | 13 | 245 | 25 | 3 | 12.0000 | |
| gduggal-bwavard | SNP | * | map_l150_m1_e0 | het | 92.8051 | 97.9602 | 88.1654 | 84.8061 | 18922 | 394 | 18699 | 2510 | 124 | 4.9402 | |
| ndellapenna-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 92.8054 | 92.7536 | 92.8571 | 88.0342 | 64 | 5 | 65 | 5 | 5 | 100.0000 | |
| astatham-gatk | SNP | ti | map_l250_m2_e0 | * | 92.8085 | 87.1006 | 99.3169 | 90.7841 | 4362 | 646 | 4362 | 30 | 12 | 40.0000 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 92.8087 | 91.4498 | 94.2085 | 69.3853 | 246 | 23 | 244 | 15 | 7 | 46.6667 | |
| asubramanian-gatk | INDEL | I16_PLUS | HG002compoundhet | * | 92.8089 | 90.2940 | 95.4680 | 54.0308 | 1935 | 208 | 1938 | 92 | 88 | 95.6522 | |
| hfeng-pmm1 | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 92.8121 | 88.0383 | 98.1333 | 66.6073 | 736 | 100 | 736 | 14 | 12 | 85.7143 | |
| jpowers-varprowl | INDEL | D1_5 | * | het | 92.8158 | 97.3223 | 88.7081 | 61.6875 | 85229 | 2345 | 85221 | 10848 | 10534 | 97.1055 | |
| gduggal-bwavard | SNP | ti | map_l150_m0_e0 | * | 92.8160 | 97.0360 | 88.9477 | 85.9871 | 7628 | 233 | 7565 | 940 | 50 | 5.3192 | |
| jmaeng-gatk | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 92.8210 | 86.6038 | 100.0000 | 44.7917 | 459 | 71 | 477 | 0 | 0 | ||
| hfeng-pmm2 | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 92.8210 | 86.6038 | 100.0000 | 48.3207 | 459 | 71 | 477 | 0 | 0 | ||
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | het | 92.8218 | 95.0820 | 90.6667 | 66.3677 | 58 | 3 | 68 | 7 | 6 | 85.7143 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 92.8220 | 96.7435 | 89.2061 | 36.1513 | 7011 | 236 | 7000 | 847 | 807 | 95.2774 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 92.8230 | 86.6071 | 100.0000 | 66.1202 | 97 | 15 | 62 | 0 | 0 | ||
| ndellapenna-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 92.8232 | 94.3471 | 91.3476 | 73.3415 | 1185 | 71 | 1193 | 113 | 71 | 62.8319 | |
| gduggal-bwafb | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 92.8240 | 87.8505 | 98.3945 | 74.4282 | 470 | 65 | 429 | 7 | 7 | 100.0000 | |
| gduggal-snapfb | SNP | ti | map_l250_m0_e0 | het | 92.8266 | 92.8266 | 92.8266 | 90.7653 | 867 | 67 | 867 | 67 | 29 | 43.2836 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 92.8267 | 87.4867 | 98.8609 | 64.0750 | 1650 | 236 | 1649 | 19 | 5 | 26.3158 | |
| jlack-gatk | INDEL | I1_5 | map_l250_m2_e1 | * | 92.8270 | 96.4912 | 89.4309 | 97.3985 | 110 | 4 | 110 | 13 | 2 | 15.3846 | |
| rpoplin-dv42 | INDEL | * | map_l100_m1_e0 | hetalt | 92.8270 | 88.7097 | 97.3451 | 88.4694 | 110 | 14 | 110 | 3 | 0 | 0.0000 | |
| gduggal-snapfb | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 92.8275 | 99.6183 | 86.9034 | 74.4470 | 783 | 3 | 783 | 118 | 3 | 2.5424 | |
| hfeng-pmm1 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 92.8280 | 87.1851 | 99.2519 | 87.9706 | 796 | 117 | 796 | 6 | 4 | 66.6667 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 92.8290 | 88.0297 | 98.1818 | 57.6923 | 831 | 113 | 54 | 1 | 1 | 100.0000 | |
| jpowers-varprowl | INDEL | * | map_l125_m2_e1 | het | 92.8294 | 93.3239 | 92.3401 | 89.9662 | 1314 | 94 | 1314 | 109 | 76 | 69.7248 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 92.8302 | 90.7619 | 94.9950 | 53.7071 | 953 | 97 | 949 | 50 | 49 | 98.0000 | |
| ckim-gatk | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 92.8310 | 87.1028 | 99.3658 | 71.0526 | 466 | 69 | 470 | 3 | 3 | 100.0000 | |
| jlack-gatk | INDEL | I1_5 | map_l125_m0_e0 | het | 92.8334 | 97.3958 | 88.6792 | 93.3977 | 187 | 5 | 188 | 24 | 0 | 0.0000 | |
| hfeng-pmm1 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 92.8361 | 88.2463 | 97.9296 | 62.5291 | 473 | 63 | 473 | 10 | 9 | 90.0000 | |
| bgallagher-sentieon | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 92.8385 | 87.0031 | 99.5129 | 39.9105 | 3327 | 497 | 3473 | 17 | 16 | 94.1176 | |
| gduggal-snapfb | INDEL | * | * | het | 92.8434 | 92.0858 | 93.6136 | 55.1298 | 178769 | 15364 | 200114 | 13652 | 5023 | 36.7931 | |
| ckim-gatk | SNP | ti | map_l100_m2_e0 | het | 92.8437 | 88.2960 | 97.8852 | 81.4673 | 27038 | 3584 | 27031 | 584 | 62 | 10.6164 | |
| mlin-fermikit | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 92.8446 | 92.0624 | 93.6403 | 70.3210 | 86952 | 7497 | 86813 | 5896 | 5729 | 97.1676 | |
| gduggal-bwaplat | SNP | ti | map_siren | het | 92.8447 | 87.2527 | 99.2026 | 72.7353 | 54430 | 7952 | 54492 | 438 | 111 | 25.3425 | |
| jpowers-varprowl | INDEL | * | map_l125_m1_e0 | het | 92.8465 | 93.3333 | 92.3647 | 89.2132 | 1246 | 89 | 1246 | 103 | 73 | 70.8738 | |
| ltrigg-rtg2 | INDEL | I1_5 | HG002compoundhet | homalt | 92.8474 | 93.6170 | 92.0904 | 71.4055 | 308 | 21 | 326 | 28 | 27 | 96.4286 | |
| ghariani-varprowl | INDEL | D1_5 | segdup | het | 92.8475 | 99.4220 | 87.0886 | 96.1448 | 688 | 4 | 688 | 102 | 61 | 59.8039 | |
| egarrison-hhga | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 92.8484 | 90.3030 | 95.5414 | 87.6863 | 149 | 16 | 150 | 7 | 5 | 71.4286 | |
| jlack-gatk | INDEL | * | segdup | het | 92.8494 | 98.6357 | 87.7044 | 96.3215 | 1446 | 20 | 1448 | 203 | 7 | 3.4483 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 92.8504 | 88.1608 | 98.0670 | 34.4871 | 3552 | 477 | 1522 | 30 | 30 | 100.0000 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 92.8514 | 86.7287 | 99.9044 | 30.7514 | 2052 | 314 | 2090 | 2 | 2 | 100.0000 | |
| gduggal-bwavard | INDEL | D1_5 | map_l100_m2_e0 | * | 92.8526 | 95.1436 | 90.6694 | 86.8647 | 1822 | 93 | 1788 | 184 | 50 | 27.1739 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 92.8529 | 99.4937 | 87.0432 | 60.7107 | 2358 | 12 | 2358 | 351 | 351 | 100.0000 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 92.8530 | 86.9868 | 99.5675 | 29.4261 | 1123 | 168 | 1151 | 5 | 5 | 100.0000 | |
| jlack-gatk | INDEL | D16_PLUS | HG002compoundhet | * | 92.8541 | 92.1401 | 93.5792 | 35.3980 | 2157 | 184 | 2157 | 148 | 143 | 96.6216 | |
| astatham-gatk | SNP | ti | map_l250_m2_e1 | * | 92.8549 | 87.1749 | 99.3266 | 90.8364 | 4425 | 651 | 4425 | 30 | 12 | 40.0000 | |
| astatham-gatk | SNP | ti | map_l125_m0_e0 | * | 92.8568 | 86.9378 | 99.6407 | 77.9287 | 11095 | 1667 | 11093 | 40 | 20 | 50.0000 | |
| ndellapenna-hhga | INDEL | I16_PLUS | * | * | 92.8570 | 90.4814 | 95.3607 | 63.8712 | 5770 | 607 | 5776 | 281 | 194 | 69.0391 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_51to200 | homalt | 92.8571 | 100.0000 | 86.6667 | 34.7826 | 13 | 0 | 13 | 2 | 1 | 50.0000 | |