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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
62901-62950 / 86044 show all | |||||||||||||||
| ckim-gatk | INDEL | * | map_l100_m1_e0 | het | 96.1061 | 98.6130 | 93.7235 | 89.8156 | 2204 | 31 | 2210 | 148 | 14 | 9.4595 | |
| ckim-gatk | INDEL | * | map_l125_m1_e0 | * | 96.6080 | 98.5287 | 94.7608 | 90.7066 | 2076 | 31 | 2080 | 115 | 11 | 9.5652 | |
| ckim-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.7528 | 96.0459 | 99.5215 | 32.8514 | 753 | 31 | 832 | 4 | 4 | 100.0000 | |
| ckim-gatk | INDEL | D1_5 | * | homalt | 99.8051 | 99.9366 | 99.6739 | 62.4819 | 48895 | 31 | 48902 | 160 | 157 | 98.1250 | |
| ckim-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 94.9615 | 90.9091 | 99.3921 | 56.0160 | 310 | 31 | 327 | 2 | 2 | 100.0000 | |
| ckim-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.8899 | 98.7393 | 99.0409 | 76.8376 | 2428 | 31 | 2375 | 23 | 14 | 60.8696 | |
| ckim-gatk | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.7119 | 99.4908 | 99.9340 | 54.5993 | 6057 | 31 | 6057 | 4 | 4 | 100.0000 | |
| ciseli-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 26.1799 | 75.0000 | 15.8576 | 76.7407 | 93 | 31 | 98 | 520 | 4 | 0.7692 | |
| cchapple-custom | INDEL | D1_5 | map_l100_m2_e0 | het | 96.0894 | 97.5318 | 94.6889 | 83.3900 | 1225 | 31 | 1248 | 70 | 7 | 10.0000 | |
| cchapple-custom | INDEL | D1_5 | map_l100_m2_e1 | het | 96.1254 | 97.5552 | 94.7368 | 83.5172 | 1237 | 31 | 1260 | 70 | 7 | 10.0000 | |
| ciseli-custom | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 63.5783 | 86.5217 | 50.2525 | 62.0690 | 199 | 31 | 199 | 197 | 181 | 91.8782 | |
| ciseli-custom | INDEL | I16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | * | 25.0000 | 16.2162 | 54.5455 | 77.0833 | 6 | 31 | 6 | 5 | 4 | 80.0000 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 81.1856 | 91.0405 | 73.2558 | 68.6589 | 315 | 31 | 315 | 115 | 55 | 47.8261 | |
| ckim-vqsr | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 99.4081 | 99.2523 | 99.5645 | 82.9173 | 4115 | 31 | 4115 | 18 | 8 | 44.4444 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 96.3472 | 95.8165 | 96.8839 | 75.3835 | 710 | 31 | 684 | 22 | 19 | 86.3636 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.3613 | 99.1592 | 99.5643 | 51.5120 | 3656 | 31 | 3656 | 16 | 13 | 81.2500 | |
| dgrover-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 97.4450 | 95.2959 | 99.6933 | 71.1249 | 628 | 31 | 650 | 2 | 2 | 100.0000 | |
| dgrover-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 97.4450 | 95.2959 | 99.6933 | 71.1249 | 628 | 31 | 650 | 2 | 2 | 100.0000 | |
| dgrover-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.9105 | 98.7393 | 99.0822 | 76.8986 | 2428 | 31 | 2375 | 22 | 13 | 59.0909 | |
| dgrover-gatk | SNP | ti | map_l150_m0_e0 | homalt | 99.3450 | 98.8772 | 99.8172 | 73.4053 | 2730 | 31 | 2730 | 5 | 4 | 80.0000 | |
| dgrover-gatk | SNP | ti | map_l250_m0_e0 | * | 97.9517 | 97.7372 | 98.1672 | 93.8664 | 1339 | 31 | 1339 | 25 | 6 | 24.0000 | |
| dgrover-gatk | SNP | ti | segdup | * | 99.6780 | 99.8413 | 99.5153 | 89.9275 | 19506 | 31 | 19504 | 95 | 6 | 6.3158 | |
| egarrison-hhga | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 80.1724 | 75.0000 | 86.1111 | 99.9462 | 93 | 31 | 93 | 15 | 8 | 53.3333 | |
| egarrison-hhga | INDEL | * | map_l125_m1_e0 | het | 97.6831 | 97.6779 | 97.6883 | 86.3886 | 1304 | 31 | 1310 | 31 | 10 | 32.2581 | |
| egarrison-hhga | INDEL | * | map_l125_m2_e0 | het | 97.7762 | 97.7714 | 97.7810 | 87.2105 | 1360 | 31 | 1366 | 31 | 10 | 32.2581 | |
| egarrison-hhga | INDEL | * | map_l125_m2_e1 | het | 97.7684 | 97.7983 | 97.7385 | 87.3174 | 1377 | 31 | 1383 | 32 | 11 | 34.3750 | |
| 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 | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 94.9615 | 90.9091 | 99.3921 | 56.0160 | 310 | 31 | 327 | 2 | 2 | 100.0000 | |
| ckim-vqsr | INDEL | I1_5 | map_l125_m2_e0 | * | 97.4066 | 96.3827 | 98.4524 | 90.8257 | 826 | 31 | 827 | 13 | 2 | 15.3846 | |
| ckim-vqsr | INDEL | I1_5 | map_l125_m2_e1 | het | 95.7853 | 93.8976 | 97.7505 | 92.7437 | 477 | 31 | 478 | 11 | 1 | 9.0909 | |
| ckim-vqsr | SNP | * | func_cds | homalt | 99.7774 | 99.5558 | 100.0000 | 21.6155 | 6948 | 31 | 6948 | 0 | 0 | ||
| egarrison-hhga | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 97.8916 | 97.7256 | 98.0583 | 70.5196 | 1332 | 31 | 1313 | 26 | 12 | 46.1538 | |
| egarrison-hhga | INDEL | I6_15 | HG002compoundhet | het | 73.2414 | 85.0962 | 64.2857 | 79.7719 | 177 | 31 | 171 | 95 | 70 | 73.6842 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 94.2276 | 93.3190 | 95.1542 | 68.0956 | 433 | 31 | 432 | 22 | 16 | 72.7273 | |
| egarrison-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 91.7694 | 88.7681 | 94.9807 | 88.6104 | 245 | 31 | 246 | 13 | 6 | 46.1538 | |
| eyeh-varpipe | INDEL | * | map_l150_m2_e0 | het | 96.7930 | 96.5784 | 97.0085 | 88.1973 | 875 | 31 | 1135 | 35 | 18 | 51.4286 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 54.9313 | 39.2157 | 91.6667 | 45.4545 | 20 | 31 | 11 | 1 | 1 | 100.0000 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 97.3004 | 96.9154 | 97.6884 | 63.0249 | 974 | 31 | 972 | 23 | 16 | 69.5652 | |
| egarrison-hhga | INDEL | D6_15 | map_l100_m1_e0 | * | 90.1237 | 87.9845 | 92.3695 | 84.8816 | 227 | 31 | 230 | 19 | 11 | 57.8947 | |
| egarrison-hhga | INDEL | D6_15 | map_l100_m2_e0 | * | 90.3524 | 88.2576 | 92.5490 | 85.5524 | 233 | 31 | 236 | 19 | 11 | 57.8947 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 98.3381 | 97.7256 | 98.9583 | 75.2486 | 1332 | 31 | 1330 | 14 | 5 | 35.7143 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 84.9618 | 80.0000 | 90.5797 | 79.6460 | 124 | 31 | 125 | 13 | 2 | 15.3846 | |
| ckim-isaac | SNP | tv | func_cds | homalt | 99.0820 | 98.1808 | 100.0000 | 21.0849 | 1673 | 31 | 1673 | 0 | 0 | ||
| ckim-vqsr | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.5126 | 99.8992 | 99.1290 | 74.4665 | 30730 | 31 | 30730 | 270 | 263 | 97.4074 | |
| ckim-isaac | INDEL | D6_15 | map_l125_m0_e0 | * | 50.0000 | 34.0426 | 94.1176 | 94.5860 | 16 | 31 | 16 | 1 | 1 | 100.0000 | |
| ckim-isaac | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 64.3678 | 47.4576 | 100.0000 | 54.8387 | 28 | 31 | 28 | 0 | 0 | ||
| hfeng-pmm2 | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.1995 | 98.5500 | 99.8576 | 35.6051 | 2107 | 31 | 2104 | 3 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.5421 | 99.7007 | 99.3840 | 44.2028 | 10326 | 31 | 10326 | 64 | 61 | 95.3125 | |
| hfeng-pmm3 | INDEL | * | map_l125_m1_e0 | * | 98.6235 | 98.5287 | 98.7186 | 85.1274 | 2076 | 31 | 2080 | 27 | 6 | 22.2222 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 99.3494 | 99.4543 | 99.2447 | 49.9340 | 5650 | 31 | 5650 | 43 | 42 | 97.6744 | |