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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
24001-24050 / 86044 show all | |||||||||||||||
| anovak-vg | INDEL | D6_15 | map_l100_m1_e0 | homalt | 82.8729 | 75.0000 | 92.5926 | 84.7025 | 48 | 16 | 50 | 4 | 4 | 100.0000 | |
| anovak-vg | INDEL | D6_15 | map_l100_m2_e0 | homalt | 83.1614 | 75.3846 | 92.7273 | 85.4111 | 49 | 16 | 51 | 4 | 4 | 100.0000 | |
| anovak-vg | INDEL | D6_15 | map_l100_m2_e1 | homalt | 82.7498 | 74.6269 | 92.8571 | 85.4167 | 50 | 17 | 52 | 4 | 4 | 100.0000 | |
| anovak-vg | INDEL | D6_15 | map_l125_m1_e0 | homalt | 84.8485 | 82.3529 | 87.5000 | 86.6109 | 28 | 6 | 28 | 4 | 4 | 100.0000 | |
| anovak-vg | INDEL | D6_15 | map_l125_m2_e0 | homalt | 85.7143 | 83.3333 | 88.2353 | 86.8726 | 30 | 6 | 30 | 4 | 4 | 100.0000 | |
| anovak-vg | INDEL | D6_15 | map_l125_m2_e1 | homalt | 86.1111 | 83.7838 | 88.5714 | 86.6412 | 31 | 6 | 31 | 4 | 4 | 100.0000 | |
| anovak-vg | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 8.0635 | 4.5113 | 37.9310 | 60.2740 | 6 | 127 | 22 | 36 | 4 | 11.1111 | |
| anovak-vg | INDEL | I16_PLUS | map_l100_m0_e0 | * | 23.5294 | 18.1818 | 33.3333 | 68.4211 | 2 | 9 | 2 | 4 | 4 | 100.0000 | |
| anovak-vg | INDEL | I16_PLUS | map_l100_m0_e0 | homalt | 0.0000 | 0.0000 | 20.0000 | 64.2857 | 0 | 2 | 1 | 4 | 4 | 100.0000 | |
| anovak-vg | INDEL | I16_PLUS | map_l125_m1_e0 | * | 27.2727 | 20.0000 | 42.8571 | 80.5556 | 3 | 12 | 3 | 4 | 4 | 100.0000 | |
| anovak-vg | INDEL | I16_PLUS | map_l125_m1_e0 | homalt | 33.3333 | 33.3333 | 33.3333 | 79.3103 | 1 | 2 | 2 | 4 | 4 | 100.0000 | |
| anovak-vg | INDEL | I16_PLUS | map_l125_m2_e0 | * | 26.0870 | 20.0000 | 37.5000 | 83.6735 | 3 | 12 | 3 | 5 | 4 | 80.0000 | |
| anovak-vg | INDEL | I16_PLUS | map_l125_m2_e0 | homalt | 30.7692 | 33.3333 | 28.5714 | 81.5789 | 1 | 2 | 2 | 5 | 4 | 80.0000 | |
| anovak-vg | INDEL | I16_PLUS | map_l125_m2_e1 | * | 26.0870 | 20.0000 | 37.5000 | 83.6735 | 3 | 12 | 3 | 5 | 4 | 80.0000 | |
| anovak-vg | INDEL | I16_PLUS | map_l125_m2_e1 | homalt | 30.7692 | 33.3333 | 28.5714 | 81.5789 | 1 | 2 | 2 | 5 | 4 | 80.0000 | |
| anovak-vg | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_51to200 | homalt | 0.0000 | 0.0000 | 20.0000 | 0 | 0 | 0 | 4 | 4 | 100.0000 | ||
| anovak-vg | INDEL | I1_5 | map_l150_m0_e0 | het | 49.5474 | 41.5094 | 61.4458 | 95.8870 | 44 | 62 | 51 | 32 | 4 | 12.5000 | |
| anovak-vg | INDEL | I6_15 | map_l125_m1_e0 | homalt | 78.7879 | 86.6667 | 72.2222 | 87.0504 | 13 | 2 | 13 | 5 | 4 | 80.0000 | |
| anovak-vg | INDEL | I6_15 | map_l125_m2_e0 | homalt | 78.7879 | 86.6667 | 72.2222 | 89.0244 | 13 | 2 | 13 | 5 | 4 | 80.0000 | |
| anovak-vg | INDEL | I6_15 | map_l125_m2_e1 | homalt | 78.7879 | 86.6667 | 72.2222 | 89.3491 | 13 | 2 | 13 | 5 | 4 | 80.0000 | |
| anovak-vg | SNP | tv | map_l250_m2_e0 | homalt | 81.7550 | 69.5838 | 99.0868 | 89.1941 | 652 | 285 | 651 | 6 | 4 | 66.6667 | |
| anovak-vg | SNP | tv | map_l250_m2_e1 | homalt | 81.8854 | 69.7674 | 99.0977 | 89.2430 | 660 | 286 | 659 | 6 | 4 | 66.6667 | |
| astatham-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.5829 | 99.5667 | 99.5991 | 76.3025 | 2987 | 13 | 2981 | 12 | 4 | 33.3333 | |
| astatham-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 87.4680 | 77.9553 | 99.6251 | 31.2943 | 976 | 276 | 1063 | 4 | 4 | 100.0000 | |
| astatham-gatk | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.9071 | 100.0000 | 99.8145 | 47.5553 | 2152 | 0 | 2152 | 4 | 4 | 100.0000 | |
| astatham-gatk | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | * | 96.1232 | 95.4955 | 96.7593 | 64.9351 | 212 | 10 | 209 | 7 | 4 | 57.1429 | |
| astatham-gatk | INDEL | * | map_l100_m0_e0 | het | 95.7071 | 94.9070 | 96.5209 | 88.5382 | 969 | 52 | 971 | 35 | 4 | 11.4286 | |
| astatham-gatk | INDEL | * | map_l125_m0_e0 | homalt | 98.6014 | 99.2958 | 97.9167 | 88.3589 | 282 | 2 | 282 | 6 | 4 | 66.6667 | |
| astatham-gatk | INDEL | * | map_l125_m1_e0 | homalt | 99.3179 | 99.4536 | 99.1826 | 86.0562 | 728 | 4 | 728 | 6 | 4 | 66.6667 | |
| astatham-gatk | INDEL | * | map_l125_m2_e0 | homalt | 99.2806 | 99.4758 | 99.0862 | 86.9395 | 759 | 4 | 759 | 7 | 4 | 57.1429 | |
| astatham-gatk | INDEL | * | map_l125_m2_e1 | homalt | 99.2908 | 99.4832 | 99.0991 | 87.0284 | 770 | 4 | 770 | 7 | 4 | 57.1429 | |
| astatham-gatk | INDEL | * | map_l150_m0_e0 | * | 96.2251 | 96.4981 | 95.9538 | 92.9541 | 496 | 18 | 498 | 21 | 4 | 19.0476 | |
| astatham-gatk | INDEL | * | map_l150_m1_e0 | het | 95.3423 | 94.3860 | 96.3183 | 91.2356 | 807 | 48 | 811 | 31 | 4 | 12.9032 | |
| astatham-gatk | INDEL | * | map_l150_m2_e0 | het | 95.2620 | 94.1501 | 96.4004 | 91.7487 | 853 | 53 | 857 | 32 | 4 | 12.5000 | |
| astatham-gatk | INDEL | * | map_l150_m2_e1 | het | 95.1831 | 93.9394 | 96.4602 | 91.7945 | 868 | 56 | 872 | 32 | 4 | 12.5000 | |
| astatham-gatk | INDEL | * | map_l150_m2_e1 | homalt | 98.9858 | 99.1870 | 98.7854 | 89.4512 | 488 | 4 | 488 | 6 | 4 | 66.6667 | |
| astatham-gatk | INDEL | * | map_l250_m1_e0 | * | 95.1613 | 96.7213 | 93.6508 | 96.0377 | 295 | 10 | 295 | 20 | 4 | 20.0000 | |
| astatham-gatk | INDEL | * | map_l250_m2_e0 | * | 95.3800 | 96.6767 | 94.1176 | 96.2801 | 320 | 11 | 320 | 20 | 4 | 20.0000 | |
| astatham-gatk | INDEL | * | map_l250_m2_e1 | * | 95.4074 | 96.6967 | 94.1520 | 96.3590 | 322 | 11 | 322 | 20 | 4 | 20.0000 | |
| astatham-gatk | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.8767 | 99.8193 | 99.9342 | 54.4187 | 6077 | 11 | 6077 | 4 | 4 | 100.0000 | |
| astatham-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 98.2387 | 96.8364 | 99.6823 | 87.5285 | 1255 | 41 | 1255 | 4 | 4 | 100.0000 | |
| astatham-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 97.7884 | 96.1222 | 99.5134 | 88.6370 | 818 | 33 | 818 | 4 | 4 | 100.0000 | |
| astatham-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 99.0127 | 98.2067 | 99.8321 | 79.0112 | 4162 | 76 | 4162 | 7 | 4 | 57.1429 | |
| astatham-gatk | SNP | ti | segdup | homalt | 99.8666 | 99.7868 | 99.9466 | 87.4281 | 7489 | 16 | 7489 | 4 | 4 | 100.0000 | |
| astatham-gatk | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.4474 | 98.9552 | 99.9444 | 60.4265 | 10797 | 114 | 10794 | 6 | 4 | 66.6667 | |
| astatham-gatk | SNP | tv | map_l100_m0_e0 | homalt | 99.2548 | 98.6999 | 99.8159 | 61.6440 | 3796 | 50 | 3796 | 7 | 4 | 57.1429 | |
| astatham-gatk | SNP | tv | map_l125_m0_e0 | homalt | 98.9564 | 98.1990 | 99.7257 | 68.9479 | 2181 | 40 | 2181 | 6 | 4 | 66.6667 | |
| astatham-gatk | SNP | tv | map_l250_m1_e0 | homalt | 98.5866 | 97.7804 | 99.4062 | 85.3845 | 837 | 19 | 837 | 5 | 4 | 80.0000 | |
| astatham-gatk | SNP | tv | map_l250_m2_e0 | homalt | 98.5460 | 97.6521 | 99.4565 | 86.4046 | 915 | 22 | 915 | 5 | 4 | 80.0000 | |
| astatham-gatk | SNP | tv | map_l250_m2_e1 | homalt | 98.5600 | 97.6744 | 99.4618 | 86.4833 | 924 | 22 | 924 | 5 | 4 | 80.0000 | |