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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
28001-28050 / 86044 show all | |||||||||||||||
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.5711 | 99.3100 | 99.8335 | 74.5893 | 3598 | 25 | 3598 | 6 | 2 | 33.3333 | |
| hfeng-pmm2 | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 84.9320 | 77.4194 | 94.0594 | 99.9207 | 96 | 28 | 95 | 6 | 0 | 0.0000 | |
| hfeng-pmm2 | INDEL | * | map_l125_m1_e0 | homalt | 99.3179 | 99.4536 | 99.1826 | 84.3929 | 728 | 4 | 728 | 6 | 4 | 66.6667 | |
| hfeng-pmm2 | INDEL | * | map_l150_m2_e1 | homalt | 98.9858 | 99.1870 | 98.7854 | 88.2938 | 488 | 4 | 488 | 6 | 4 | 66.6667 | |
| jlack-gatk | INDEL | I16_PLUS | map_siren | * | 94.2920 | 95.3488 | 93.2584 | 92.8743 | 82 | 4 | 83 | 6 | 1 | 16.6667 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 95.3273 | 91.1635 | 99.8897 | 40.2875 | 5375 | 521 | 5435 | 6 | 5 | 83.3333 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 97.6744 | 97.1098 | 98.2456 | 68.8808 | 336 | 10 | 336 | 6 | 3 | 50.0000 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 95.3273 | 91.1635 | 99.8897 | 40.2875 | 5375 | 521 | 5435 | 6 | 5 | 83.3333 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 38.6555 | 85.1852 | 25.0000 | 93.6508 | 23 | 4 | 2 | 6 | 0 | 0.0000 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.4903 | 99.4178 | 99.5630 | 74.2111 | 1366 | 8 | 1367 | 6 | 0 | 0.0000 | |
| jlack-gatk | INDEL | I1_5 | map_l250_m0_e0 | * | 84.6154 | 91.6667 | 78.5714 | 98.6090 | 22 | 2 | 22 | 6 | 1 | 16.6667 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.4292 | 98.1557 | 98.7041 | 82.3820 | 479 | 9 | 457 | 6 | 2 | 33.3333 | |
| jlack-gatk | INDEL | I6_15 | map_l125_m1_e0 | het | 83.8710 | 86.6667 | 81.2500 | 93.6759 | 26 | 4 | 26 | 6 | 0 | 0.0000 | |
| jlack-gatk | INDEL | I6_15 | map_l125_m2_e0 | het | 83.8710 | 86.6667 | 81.2500 | 94.3860 | 26 | 4 | 26 | 6 | 0 | 0.0000 | |
| jlack-gatk | INDEL | I6_15 | map_l125_m2_e1 | het | 83.8710 | 86.6667 | 81.2500 | 94.5299 | 26 | 4 | 26 | 6 | 0 | 0.0000 | |
| jlack-gatk | SNP | ti | HG002compoundhet | homalt | 99.8918 | 99.8648 | 99.9188 | 30.3225 | 7384 | 10 | 7384 | 6 | 6 | 100.0000 | |
| jlack-gatk | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.8910 | 99.8415 | 99.9405 | 60.8743 | 10081 | 16 | 10081 | 6 | 6 | 100.0000 | |
| jlack-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.6673 | 99.4468 | 99.8889 | 71.7685 | 5393 | 30 | 5393 | 6 | 6 | 100.0000 | |
| jlack-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.6673 | 99.4468 | 99.8889 | 71.7685 | 5393 | 30 | 5393 | 6 | 6 | 100.0000 | |
| jlack-gatk | SNP | tv | map_l150_m0_e0 | homalt | 98.4393 | 97.3645 | 99.5381 | 76.5184 | 1293 | 35 | 1293 | 6 | 4 | 66.6667 | |
| jlack-gatk | SNP | tv | segdup | homalt | 99.8611 | 99.9074 | 99.8149 | 89.7982 | 3235 | 3 | 3235 | 6 | 6 | 100.0000 | |
| jli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 99.7085 | 99.7349 | 99.6820 | 71.4048 | 1881 | 5 | 1881 | 6 | 3 | 50.0000 | |
| jli-custom | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 97.3074 | 94.9664 | 99.7667 | 39.5535 | 2547 | 135 | 2566 | 6 | 6 | 100.0000 | |
| jli-custom | INDEL | * | map_l125_m1_e0 | homalt | 99.2491 | 99.3169 | 99.1814 | 84.5684 | 727 | 5 | 727 | 6 | 4 | 66.6667 | |
| jli-custom | INDEL | * | map_l150_m2_e1 | homalt | 98.8832 | 98.9837 | 98.7830 | 88.3699 | 487 | 5 | 487 | 6 | 4 | 66.6667 | |
| jli-custom | INDEL | * | map_l250_m0_e0 | het | 91.7431 | 94.3396 | 89.2857 | 97.4110 | 50 | 3 | 50 | 6 | 1 | 16.6667 | |
| hfeng-pmm1 | INDEL | * | map_l150_m2_e0 | homalt | 98.8577 | 98.9605 | 98.7552 | 88.0545 | 476 | 5 | 476 | 6 | 3 | 50.0000 | |
| hfeng-pmm1 | INDEL | * | map_l150_m2_e1 | homalt | 98.8832 | 98.9837 | 98.7830 | 88.0630 | 487 | 5 | 487 | 6 | 3 | 50.0000 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.1495 | 99.0291 | 99.2701 | 69.1789 | 816 | 8 | 816 | 6 | 1 | 16.6667 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | het | 96.5155 | 98.1707 | 94.9153 | 85.9857 | 161 | 3 | 112 | 6 | 6 | 100.0000 | |
| hfeng-pmm1 | INDEL | D16_PLUS | map_l100_m0_e0 | * | 86.6667 | 92.8571 | 81.2500 | 94.6932 | 26 | 2 | 26 | 6 | 0 | 0.0000 | |
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 98.2781 | 97.3753 | 99.1979 | 63.8123 | 742 | 20 | 742 | 6 | 1 | 16.6667 | |
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 98.3871 | 98.1609 | 98.6143 | 65.7437 | 427 | 8 | 427 | 6 | 1 | 16.6667 | |
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 80.8789 | 71.8519 | 92.5000 | 74.9216 | 97 | 38 | 74 | 6 | 4 | 66.6667 | |
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.2959 | 98.6897 | 99.9096 | 50.3888 | 6628 | 88 | 6630 | 6 | 3 | 50.0000 | |
| hfeng-pmm1 | INDEL | D1_5 | map_l150_m1_e0 | * | 97.8825 | 96.6527 | 99.1441 | 85.9378 | 693 | 24 | 695 | 6 | 1 | 16.6667 | |
| hfeng-pmm1 | INDEL | D1_5 | map_l150_m2_e0 | * | 98.0117 | 96.8545 | 99.1968 | 86.8347 | 739 | 24 | 741 | 6 | 1 | 16.6667 | |
| hfeng-pmm1 | INDEL | D1_5 | map_l150_m2_e1 | * | 97.9841 | 96.7866 | 99.2116 | 86.8612 | 753 | 25 | 755 | 6 | 1 | 16.6667 | |
| hfeng-pmm1 | INDEL | D1_5 | segdup | * | 99.4565 | 99.4560 | 99.4570 | 94.0511 | 1097 | 6 | 1099 | 6 | 0 | 0.0000 | |
| hfeng-pmm1 | INDEL | D1_5 | segdup | het | 99.2064 | 99.2775 | 99.1354 | 93.9383 | 687 | 5 | 688 | 6 | 0 | 0.0000 | |
| hfeng-pmm1 | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.3163 | 97.0393 | 99.6273 | 57.4974 | 1606 | 49 | 1604 | 6 | 3 | 50.0000 | |
| hfeng-pmm1 | INDEL | I16_PLUS | * | hetalt | 96.1260 | 92.8027 | 99.6962 | 58.0768 | 1947 | 151 | 1969 | 6 | 6 | 100.0000 | |
| hfeng-pmm1 | INDEL | I16_PLUS | HG002complexvar | homalt | 99.0385 | 100.0000 | 98.0952 | 70.1139 | 309 | 0 | 309 | 6 | 5 | 83.3333 | |
| hfeng-pmm1 | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.2643 | 91.7476 | 96.9231 | 87.6033 | 189 | 17 | 189 | 6 | 2 | 33.3333 | |
| hfeng-pmm1 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 95.7835 | 93.2367 | 98.4733 | 73.1190 | 386 | 28 | 387 | 6 | 4 | 66.6667 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 97.9710 | 97.6879 | 98.2558 | 68.8688 | 338 | 8 | 338 | 6 | 0 | 0.0000 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 98.7719 | 98.5989 | 98.9455 | 64.4153 | 563 | 8 | 563 | 6 | 6 | 100.0000 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.8185 | 95.8304 | 99.8909 | 57.5027 | 5493 | 239 | 5494 | 6 | 4 | 66.6667 | |
| hfeng-pmm2 | INDEL | D16_PLUS | HG002complexvar | homalt | 98.1002 | 98.2699 | 97.9310 | 75.1286 | 284 | 5 | 284 | 6 | 5 | 83.3333 | |
| hfeng-pmm2 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 98.9653 | 98.6650 | 99.2674 | 69.4858 | 813 | 11 | 813 | 6 | 1 | 16.6667 | |