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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
60801-60850 / 86044 show all | |||||||||||||||
| ckim-vqsr | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | het | 99.7614 | 99.6188 | 99.9044 | 71.9607 | 3136 | 12 | 3136 | 3 | 3 | 100.0000 | |
| ckim-vqsr | SNP | ti | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.5515 | 99.1544 | 99.9518 | 47.1169 | 6215 | 53 | 6215 | 3 | 3 | 100.0000 | |
| ckim-vqsr | SNP | ti | lowcmp_SimpleRepeat_quadTR_51to200 | * | 93.3333 | 90.0990 | 96.8085 | 93.6314 | 91 | 10 | 91 | 3 | 3 | 100.0000 | |
| ckim-vqsr | SNP | ti | lowcmp_SimpleRepeat_quadTR_51to200 | het | 93.8462 | 92.4242 | 95.3125 | 93.8402 | 61 | 5 | 61 | 3 | 3 | 100.0000 | |
| ckim-vqsr | SNP | ti | map_l100_m1_e0 | homalt | 61.0965 | 43.9922 | 99.9620 | 75.5921 | 7901 | 10059 | 7901 | 3 | 3 | 100.0000 | |
| ckim-vqsr | SNP | ti | map_l100_m2_e0 | homalt | 61.7649 | 44.6884 | 99.9633 | 77.1942 | 8182 | 10127 | 8182 | 3 | 3 | 100.0000 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.7528 | 96.0459 | 99.5215 | 32.8514 | 753 | 31 | 832 | 4 | 4 | 100.0000 | |
| ckim-vqsr | INDEL | D16_PLUS | map_l100_m1_e0 | * | 89.8876 | 91.9540 | 87.9121 | 95.3737 | 80 | 7 | 80 | 11 | 4 | 36.3636 | |
| ckim-vqsr | INDEL | D16_PLUS | map_l100_m1_e0 | het | 88.7014 | 95.6522 | 82.6923 | 96.3989 | 44 | 2 | 43 | 9 | 4 | 44.4444 | |
| ckim-vqsr | INDEL | D16_PLUS | map_l100_m2_e0 | * | 90.2174 | 92.2222 | 88.2979 | 95.8952 | 83 | 7 | 83 | 11 | 4 | 36.3636 | |
| ckim-vqsr | INDEL | D16_PLUS | map_l100_m2_e0 | het | 88.9670 | 95.8333 | 83.0189 | 96.8187 | 46 | 2 | 44 | 9 | 4 | 44.4444 | |
| ckim-vqsr | INDEL | D16_PLUS | map_l100_m2_e1 | * | 90.3553 | 91.7526 | 89.0000 | 95.7301 | 89 | 8 | 89 | 11 | 4 | 36.3636 | |
| ckim-vqsr | INDEL | D16_PLUS | map_l100_m2_e1 | het | 89.5935 | 96.0784 | 83.9286 | 96.7136 | 49 | 2 | 47 | 9 | 4 | 44.4444 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 98.6239 | 98.8506 | 98.3982 | 70.2519 | 430 | 5 | 430 | 7 | 4 | 57.1429 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.9182 | 99.9454 | 99.8909 | 51.3011 | 3664 | 2 | 3664 | 4 | 4 | 100.0000 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 97.8966 | 96.4615 | 99.3750 | 22.2357 | 627 | 23 | 636 | 4 | 4 | 100.0000 | |
| ckim-vqsr | INDEL | D1_5 | map_l100_m0_e0 | * | 96.7071 | 96.9873 | 96.4286 | 89.7798 | 837 | 26 | 837 | 31 | 4 | 12.9032 | |
| ckim-vqsr | INDEL | D1_5 | map_l100_m1_e0 | het | 96.5230 | 96.3606 | 96.6860 | 89.4465 | 1165 | 44 | 1167 | 40 | 4 | 10.0000 | |
| ckim-vqsr | INDEL | D1_5 | map_l100_m2_e0 | het | 96.5708 | 96.3376 | 96.8051 | 89.9162 | 1210 | 46 | 1212 | 40 | 4 | 10.0000 | |
| ckim-vqsr | INDEL | D1_5 | map_l100_m2_e1 | het | 96.5215 | 96.2145 | 96.8304 | 89.9905 | 1220 | 48 | 1222 | 40 | 4 | 10.0000 | |
| ckim-vqsr | INDEL | D1_5 | map_l150_m1_e0 | * | 96.0363 | 96.2343 | 95.8391 | 92.4668 | 690 | 27 | 691 | 30 | 4 | 13.3333 | |
| ckim-vqsr | INDEL | D1_5 | map_l150_m2_e0 | * | 96.0079 | 96.0682 | 95.9477 | 92.8545 | 733 | 30 | 734 | 31 | 4 | 12.9032 | |
| ckim-vqsr | INDEL | D1_5 | map_siren | homalt | 99.4864 | 99.4007 | 99.5723 | 81.4444 | 1161 | 7 | 1164 | 5 | 4 | 80.0000 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 98.7147 | 100.0000 | 97.4619 | 47.3262 | 192 | 0 | 192 | 5 | 4 | 80.0000 | |
| ckim-vqsr | INDEL | D6_15 | segdup | * | 96.0630 | 95.8115 | 96.3158 | 95.0955 | 183 | 8 | 183 | 7 | 4 | 57.1429 | |
| ckim-vqsr | INDEL | D6_15 | segdup | homalt | 96.1538 | 100.0000 | 92.5926 | 92.3944 | 50 | 0 | 50 | 4 | 4 | 100.0000 | |
| ckim-vqsr | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | het | 94.0845 | 91.8750 | 96.4029 | 90.0144 | 147 | 13 | 134 | 5 | 4 | 80.0000 | |
| ckim-vqsr | INDEL | I1_5 | HG002complexvar | hetalt | 92.1493 | 85.6315 | 99.7409 | 68.7323 | 1478 | 248 | 1540 | 4 | 4 | 100.0000 | |
| ckim-vqsr | INDEL | I1_5 | HG002compoundhet | hetalt | 95.5975 | 91.5988 | 99.9612 | 55.8418 | 10238 | 939 | 10299 | 4 | 4 | 100.0000 | |
| ckim-vqsr | INDEL | I1_5 | map_l100_m1_e0 | * | 97.7372 | 96.7140 | 98.7823 | 87.5119 | 1295 | 44 | 1298 | 16 | 4 | 25.0000 | |
| ckim-vqsr | INDEL | I1_5 | map_l100_m2_e0 | * | 97.7479 | 96.7105 | 98.8077 | 88.3990 | 1323 | 45 | 1326 | 16 | 4 | 25.0000 | |
| ckim-vqsr | INDEL | I1_5 | map_l100_m2_e1 | * | 97.7178 | 96.6308 | 98.8296 | 88.4427 | 1348 | 47 | 1351 | 16 | 4 | 25.0000 | |
| ckim-vqsr | INDEL | I6_15 | HG002complexvar | het | 99.2942 | 98.8110 | 99.7821 | 59.6661 | 2327 | 28 | 2290 | 5 | 4 | 80.0000 | |
| ckim-vqsr | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.6029 | 93.5337 | 99.8803 | 39.4384 | 3298 | 228 | 3339 | 4 | 4 | 100.0000 | |
| ckim-vqsr | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.3956 | 93.1863 | 99.8338 | 31.7550 | 2366 | 173 | 2403 | 4 | 4 | 100.0000 | |
| ckim-vqsr | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 96.3003 | 93.0030 | 99.8400 | 33.3511 | 2459 | 185 | 2496 | 4 | 4 | 100.0000 | |
| ckim-vqsr | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.6029 | 93.5337 | 99.8803 | 39.4384 | 3298 | 228 | 3339 | 4 | 4 | 100.0000 | |
| ckim-vqsr | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 97.3822 | 96.3731 | 98.4127 | 91.0490 | 372 | 14 | 372 | 6 | 4 | 66.6667 | |
| ckim-vqsr | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 97.0803 | 96.3768 | 97.7941 | 91.0703 | 266 | 10 | 266 | 6 | 4 | 66.6667 | |
| ckim-vqsr | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.6562 | 99.3685 | 99.9455 | 58.6114 | 11014 | 70 | 11010 | 6 | 4 | 66.6667 | |
| ckim-vqsr | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.3474 | 98.7681 | 99.9335 | 54.7798 | 6013 | 75 | 6013 | 4 | 4 | 100.0000 | |
| ckim-vqsr | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.5978 | 99.3202 | 99.8769 | 36.6057 | 7305 | 50 | 7301 | 9 | 4 | 44.4444 | |
| ckim-vqsr | SNP | * | map_l125_m2_e0 | het | 81.2064 | 69.0122 | 98.6348 | 89.1411 | 20233 | 9085 | 20230 | 280 | 4 | 1.4286 | |
| ckim-vqsr | SNP | * | map_l125_m2_e1 | het | 81.3082 | 69.1532 | 98.6474 | 89.1453 | 20497 | 9143 | 20494 | 281 | 4 | 1.4235 | |
| ckim-vqsr | SNP | * | map_siren | homalt | 75.3334 | 60.4322 | 99.9880 | 62.9988 | 33332 | 21824 | 33323 | 4 | 4 | 100.0000 | |
| ckim-vqsr | SNP | * | segdup | het | 98.9505 | 98.5621 | 99.3421 | 95.0542 | 17068 | 249 | 17062 | 113 | 4 | 3.5398 | |
| ckim-vqsr | SNP | ti | HG002compoundhet | homalt | 98.6436 | 97.3763 | 99.9445 | 31.0556 | 7200 | 194 | 7200 | 4 | 4 | 100.0000 | |
| ckim-vqsr | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 99.5016 | 99.4565 | 99.5467 | 86.5782 | 1098 | 6 | 1098 | 5 | 4 | 80.0000 | |
| ckim-vqsr | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 99.4452 | 99.5833 | 99.3075 | 87.8041 | 717 | 3 | 717 | 5 | 4 | 80.0000 | |
| egarrison-hhga | INDEL | * | map_siren | hetalt | 84.9102 | 75.3036 | 97.3262 | 88.3489 | 186 | 61 | 182 | 5 | 4 | 80.0000 | |