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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
29251-29300 / 86044 show all | |||||||||||||||
| ghariani-varprowl | SNP | tv | map_l250_m2_e1 | homalt | 97.8518 | 96.3002 | 99.4541 | 89.6696 | 911 | 35 | 911 | 5 | 1 | 20.0000 | |
| hfeng-pmm1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.6820 | 99.5032 | 99.8615 | 74.2124 | 3605 | 18 | 3605 | 5 | 1 | 20.0000 | |
| hfeng-pmm1 | INDEL | * | map_l125_m0_e0 | homalt | 98.5965 | 98.9437 | 98.2517 | 86.4967 | 281 | 3 | 281 | 5 | 3 | 60.0000 | |
| asubramanian-gatk | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 98.6791 | 97.8831 | 99.4882 | 71.3069 | 971 | 21 | 972 | 5 | 2 | 40.0000 | |
| bgallagher-sentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.8363 | 99.9065 | 99.7662 | 76.2965 | 2136 | 2 | 2134 | 5 | 1 | 20.0000 | |
| bgallagher-sentieon | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.7400 | 99.6173 | 99.8629 | 52.8317 | 3644 | 14 | 3643 | 5 | 1 | 20.0000 | |
| bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 98.9825 | 99.0991 | 98.8662 | 75.3356 | 440 | 4 | 436 | 5 | 0 | 0.0000 | |
| bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.5924 | 95.7627 | 99.4934 | 31.8370 | 904 | 40 | 982 | 5 | 5 | 100.0000 | |
| bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 96.5857 | 94.5714 | 98.6877 | 35.6419 | 331 | 19 | 376 | 5 | 5 | 100.0000 | |
| bgallagher-sentieon | INDEL | D16_PLUS | map_l100_m0_e0 | het | 85.1182 | 94.7368 | 77.2727 | 96.5300 | 18 | 1 | 17 | 5 | 0 | 0.0000 | |
| bgallagher-sentieon | INDEL | D16_PLUS | map_l100_m1_e0 | homalt | 82.3529 | 93.3333 | 73.6842 | 95.2141 | 14 | 1 | 14 | 5 | 0 | 0.0000 | |
| bgallagher-sentieon | INDEL | D16_PLUS | map_l100_m2_e0 | homalt | 83.3333 | 93.7500 | 75.0000 | 95.8071 | 15 | 1 | 15 | 5 | 0 | 0.0000 | |
| bgallagher-sentieon | INDEL | D16_PLUS | map_l100_m2_e1 | homalt | 83.3333 | 93.7500 | 75.0000 | 95.8420 | 15 | 1 | 15 | 5 | 0 | 0.0000 | |
| bgallagher-sentieon | INDEL | D16_PLUS | map_siren | homalt | 91.6667 | 97.0588 | 86.8421 | 94.0157 | 33 | 1 | 33 | 5 | 0 | 0.0000 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 92.7196 | 86.7545 | 99.5656 | 30.9538 | 1120 | 171 | 1146 | 5 | 4 | 80.0000 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 97.7416 | 96.3077 | 99.2188 | 22.9844 | 626 | 24 | 635 | 5 | 4 | 80.0000 | |
| anovak-vg | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | het | 52.8000 | 37.9310 | 86.8421 | 99.9569 | 33 | 54 | 33 | 5 | 5 | 100.0000 | |
| anovak-vg | INDEL | C1_5 | HG002compoundhet | homalt | 0.0000 | 0.0000 | 28.5714 | 81.0811 | 0 | 0 | 2 | 5 | 4 | 80.0000 | |
| anovak-vg | INDEL | C1_5 | map_l100_m1_e0 | * | 0.0000 | 0.0000 | 37.5000 | 96.7742 | 0 | 0 | 3 | 5 | 0 | 0.0000 | |
| anovak-vg | INDEL | C1_5 | map_l100_m1_e0 | het | 0.0000 | 0.0000 | 28.5714 | 96.7442 | 0 | 0 | 2 | 5 | 0 | 0.0000 | |
| anovak-vg | INDEL | C1_5 | map_l100_m2_e0 | * | 0.0000 | 0.0000 | 37.5000 | 97.1326 | 0 | 0 | 3 | 5 | 0 | 0.0000 | |
| anovak-vg | INDEL | C1_5 | map_l100_m2_e0 | het | 0.0000 | 0.0000 | 28.5714 | 97.1193 | 0 | 0 | 2 | 5 | 0 | 0.0000 | |
| anovak-vg | INDEL | C1_5 | map_l100_m2_e1 | * | 0.0000 | 0.0000 | 37.5000 | 97.1429 | 0 | 0 | 3 | 5 | 0 | 0.0000 | |
| anovak-vg | INDEL | C1_5 | map_l100_m2_e1 | het | 0.0000 | 0.0000 | 28.5714 | 97.1311 | 0 | 0 | 2 | 5 | 0 | 0.0000 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 83.8725 | 78.8462 | 89.5833 | 67.1233 | 41 | 11 | 43 | 5 | 2 | 40.0000 | |
| anovak-vg | INDEL | D1_5 | map_l150_m0_e0 | homalt | 79.2389 | 69.4118 | 92.3077 | 92.5373 | 59 | 26 | 60 | 5 | 4 | 80.0000 | |
| anovak-vg | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_gt10 | het | 55.3846 | 42.8571 | 78.2609 | 99.2474 | 18 | 24 | 18 | 5 | 5 | 100.0000 | |
| anovak-vg | INDEL | D6_15 | segdup | homalt | 85.5227 | 82.0000 | 89.3617 | 91.4234 | 41 | 9 | 42 | 5 | 3 | 60.0000 | |
| 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 | |
| astatham-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.9231 | 96.3983 | 99.4970 | 32.0574 | 910 | 34 | 989 | 5 | 5 | 100.0000 | |
| astatham-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 99.3534 | 99.7835 | 98.9270 | 63.9598 | 461 | 1 | 461 | 5 | 5 | 100.0000 | |
| astatham-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 94.9640 | 97.0588 | 92.9577 | 96.7356 | 66 | 2 | 66 | 5 | 0 | 0.0000 | |
| astatham-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_gt10 | het | 92.3077 | 95.4545 | 89.3617 | 96.6284 | 42 | 2 | 42 | 5 | 0 | 0.0000 | |
| astatham-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 96.8861 | 95.1429 | 98.6945 | 35.5219 | 333 | 17 | 378 | 5 | 5 | 100.0000 | |
| astatham-gatk | INDEL | D16_PLUS | map_l100_m0_e0 | * | 86.2069 | 89.2857 | 83.3333 | 96.8051 | 25 | 3 | 25 | 5 | 0 | 0.0000 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 93.7749 | 88.6135 | 99.5748 | 31.3084 | 1144 | 147 | 1171 | 5 | 5 | 100.0000 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.9182 | 99.9727 | 99.8638 | 51.1578 | 3665 | 1 | 3665 | 5 | 5 | 100.0000 | |
| astatham-gatk | INDEL | D1_5 | map_siren | homalt | 99.6154 | 99.6575 | 99.5734 | 81.2660 | 1164 | 4 | 1167 | 5 | 4 | 80.0000 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 98.7147 | 100.0000 | 97.4619 | 47.3262 | 192 | 0 | 192 | 5 | 4 | 80.0000 | |
| astatham-gatk | INDEL | D6_15 | map_l100_m0_e0 | * | 96.1538 | 97.0874 | 95.2381 | 90.1961 | 100 | 3 | 100 | 5 | 1 | 20.0000 | |
| astatham-gatk | INDEL | D6_15 | map_l100_m0_e0 | het | 95.1613 | 98.3333 | 92.1875 | 91.2449 | 59 | 1 | 59 | 5 | 1 | 20.0000 | |
| astatham-gatk | INDEL | I16_PLUS | * | hetalt | 96.0726 | 92.6597 | 99.7466 | 58.1637 | 1944 | 154 | 1968 | 5 | 5 | 100.0000 | |
| astatham-gatk | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 95.8025 | 94.1748 | 97.4874 | 88.3010 | 194 | 12 | 194 | 5 | 2 | 40.0000 | |
| astatham-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 89.7959 | 100.0000 | 81.4815 | 87.6147 | 22 | 0 | 22 | 5 | 5 | 100.0000 | |
| astatham-gatk | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | het | 95.4274 | 94.3750 | 96.5035 | 89.8148 | 151 | 9 | 138 | 5 | 4 | 80.0000 | |
| astatham-gatk | INDEL | I16_PLUS | map_siren | het | 93.0693 | 95.9184 | 90.3846 | 91.9255 | 47 | 2 | 47 | 5 | 0 | 0.0000 | |
| astatham-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.5149 | 99.5000 | 97.5490 | 60.7692 | 199 | 1 | 199 | 5 | 5 | 100.0000 | |