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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
36051-36100 / 86044 show all | |||||||||||||||
| hfeng-pmm1 | INDEL | * | map_l250_m0_e0 | * | 92.4051 | 93.5897 | 91.2500 | 97.0717 | 73 | 5 | 73 | 7 | 2 | 28.5714 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.6156 | 99.4518 | 99.7800 | 65.1991 | 907 | 5 | 907 | 2 | 1 | 50.0000 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 96.7604 | 97.5124 | 96.0199 | 87.0988 | 196 | 5 | 193 | 8 | 1 | 12.5000 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 97.6608 | 97.0930 | 98.2353 | 79.4686 | 167 | 5 | 167 | 3 | 1 | 33.3333 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 98.9812 | 98.8739 | 99.0888 | 73.5383 | 439 | 5 | 435 | 4 | 0 | 0.0000 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 98.2592 | 98.0695 | 98.4496 | 56.8562 | 254 | 5 | 254 | 4 | 3 | 75.0000 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_51to200 | * | 93.1818 | 89.1304 | 97.6190 | 65.2893 | 41 | 5 | 41 | 1 | 1 | 100.0000 | |
| hfeng-pmm1 | INDEL | D16_PLUS | map_l100_m2_e1 | hetalt | 90.9091 | 83.3333 | 100.0000 | 77.6860 | 25 | 5 | 27 | 0 | 0 | ||
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_51to200 | hetalt | 94.6237 | 89.7959 | 100.0000 | 27.8689 | 44 | 5 | 44 | 0 | 0 | ||
| hfeng-pmm1 | INDEL | D1_5 | map_siren | homalt | 99.7001 | 99.5719 | 99.8286 | 78.3166 | 1163 | 5 | 1165 | 2 | 2 | 100.0000 | |
| 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_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.6516 | 99.4206 | 99.8837 | 61.5213 | 858 | 5 | 859 | 1 | 1 | 100.0000 | |
| hfeng-pmm1 | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_51to200 | * | 97.8546 | 96.4789 | 99.2701 | 42.4370 | 137 | 5 | 136 | 1 | 1 | 100.0000 | |
| hfeng-pmm1 | INDEL | D6_15 | map_l125_m1_e0 | * | 97.8166 | 95.7265 | 100.0000 | 88.0342 | 112 | 5 | 112 | 0 | 0 | ||
| hfeng-pmm1 | INDEL | D6_15 | map_siren | het | 98.2111 | 98.2143 | 98.2079 | 83.3333 | 275 | 5 | 274 | 5 | 1 | 20.0000 | |
| hfeng-pmm1 | INDEL | D6_15 | segdup | het | 96.1326 | 94.5652 | 97.7528 | 94.0067 | 87 | 5 | 87 | 2 | 0 | 0.0000 | |
| hfeng-pmm1 | INDEL | I16_PLUS | * | homalt | 98.2323 | 99.6797 | 96.8264 | 69.2499 | 1556 | 5 | 1556 | 51 | 49 | 96.0784 | |
| hfeng-pmm1 | INDEL | I16_PLUS | HG002compoundhet | het | 88.6756 | 89.3617 | 88.0000 | 93.8725 | 42 | 5 | 22 | 3 | 2 | 66.6667 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 97.7169 | 95.5357 | 100.0000 | 75.9551 | 107 | 5 | 107 | 0 | 0 | ||
| jlack-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 96.8349 | 99.1243 | 94.6488 | 66.0998 | 566 | 5 | 566 | 32 | 32 | 100.0000 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 93.5774 | 90.1961 | 97.2222 | 93.7282 | 46 | 5 | 35 | 1 | 0 | 0.0000 | |
| jlack-gatk | INDEL | I1_5 | map_l125_m0_e0 | * | 94.8813 | 98.3871 | 91.6168 | 91.9265 | 305 | 5 | 306 | 28 | 2 | 7.1429 | |
| 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 | |
| jlack-gatk | INDEL | I1_5 | map_l150_m0_e0 | * | 94.4979 | 97.1591 | 91.9786 | 94.4724 | 171 | 5 | 172 | 15 | 2 | 13.3333 | |
| jlack-gatk | INDEL | I1_5 | map_l150_m0_e0 | het | 91.8714 | 95.2830 | 88.6957 | 95.6977 | 101 | 5 | 102 | 13 | 0 | 0.0000 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 98.2857 | 97.1751 | 99.4220 | 74.4838 | 172 | 5 | 172 | 1 | 1 | 100.0000 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 98.5464 | 97.9339 | 99.1667 | 69.3878 | 237 | 5 | 238 | 2 | 2 | 100.0000 | |
| jlack-gatk | INDEL | I6_15 | map_l100_m1_e0 | het | 89.2562 | 91.5254 | 87.0968 | 90.7186 | 54 | 5 | 54 | 8 | 0 | 0.0000 | |
| jlack-gatk | INDEL | I6_15 | map_l100_m2_e0 | het | 89.6000 | 91.8033 | 87.5000 | 91.2688 | 56 | 5 | 56 | 8 | 0 | 0.0000 | |
| jlack-gatk | INDEL | I6_15 | map_l100_m2_e1 | het | 89.6000 | 91.8033 | 87.5000 | 91.4894 | 56 | 5 | 56 | 8 | 0 | 0.0000 | |
| jlack-gatk | INDEL | I6_15 | map_l125_m1_e0 | * | 88.0734 | 90.5660 | 85.7143 | 92.6606 | 48 | 5 | 48 | 8 | 0 | 0.0000 | |
| jlack-gatk | INDEL | I6_15 | map_l125_m2_e0 | * | 88.0734 | 90.5660 | 85.7143 | 93.5409 | 48 | 5 | 48 | 8 | 0 | 0.0000 | |
| jlack-gatk | INDEL | I6_15 | map_l125_m2_e1 | * | 88.0734 | 90.5660 | 85.7143 | 93.7079 | 48 | 5 | 48 | 8 | 0 | 0.0000 | |
| jlack-gatk | INDEL | I6_15 | map_siren | hetalt | 96.4029 | 93.0556 | 100.0000 | 78.5256 | 67 | 5 | 67 | 0 | 0 | ||
| jlack-gatk | SNP | * | * | hetalt | 99.0280 | 99.4259 | 98.6333 | 53.8866 | 866 | 5 | 866 | 12 | 11 | 91.6667 | |
| jlack-gatk | SNP | * | HG002compoundhet | hetalt | 99.6512 | 99.4200 | 99.8834 | 22.4231 | 857 | 5 | 857 | 1 | 1 | 100.0000 | |
| jlack-gatk | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.9333 | 99.9259 | 99.9407 | 34.6955 | 6740 | 5 | 6740 | 4 | 3 | 75.0000 | |
| jlack-gatk | SNP | * | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 93.5065 | 87.8049 | 100.0000 | 92.8713 | 36 | 5 | 36 | 0 | 0 | ||
| jlack-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.6270 | 99.8753 | 99.3798 | 50.2161 | 4006 | 5 | 4006 | 25 | 1 | 4.0000 | |
| jlack-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 98.6014 | 99.4125 | 97.8035 | 88.8214 | 846 | 5 | 846 | 19 | 8 | 42.1053 | |
| jlack-gatk | SNP | ti | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 92.3077 | 85.7143 | 100.0000 | 92.7885 | 30 | 5 | 30 | 0 | 0 | ||
| jlack-gatk | SNP | tv | * | hetalt | 99.0280 | 99.4259 | 98.6333 | 53.8866 | 866 | 5 | 866 | 12 | 11 | 91.6667 | |
| jlack-gatk | SNP | tv | HG002compoundhet | hetalt | 99.6512 | 99.4200 | 99.8834 | 22.4231 | 857 | 5 | 857 | 1 | 1 | 100.0000 | |
| jlack-gatk | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.3650 | 99.8551 | 98.8796 | 40.1582 | 3445 | 5 | 3442 | 39 | 2 | 5.1282 | |
| 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_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.8361 | 99.7661 | 99.9062 | 74.5708 | 2133 | 5 | 2131 | 2 | 1 | 50.0000 | |
| jli-custom | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.9292 | 99.9557 | 99.9027 | 55.9852 | 11291 | 5 | 11292 | 11 | 11 | 100.0000 | |
| jli-custom | INDEL | * | map_l100_m0_e0 | hetalt | 90.3728 | 84.8485 | 96.6667 | 91.4040 | 28 | 5 | 29 | 1 | 0 | 0.0000 | |
| 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_l125_m2_e0 | homalt | 99.2147 | 99.3447 | 99.0850 | 85.6014 | 758 | 5 | 758 | 7 | 4 | 57.1429 | |