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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
14151-14200 / 86044 show all | |||||||||||||||
| jmaeng-gatk | INDEL | D16_PLUS | HG002complexvar | homalt | 98.6254 | 99.3080 | 97.9522 | 75.9046 | 287 | 2 | 287 | 6 | 5 | 83.3333 | |
| hfeng-pmm2 | INDEL | D1_5 | map_l150_m0_e0 | * | 97.4608 | 99.3080 | 95.6811 | 91.3754 | 287 | 2 | 288 | 13 | 1 | 7.6923 | |
| hfeng-pmm3 | INDEL | D1_5 | map_l150_m0_e0 | * | 98.4604 | 99.3080 | 97.6271 | 89.5723 | 287 | 2 | 288 | 7 | 1 | 14.2857 | |
| jli-custom | INDEL | D16_PLUS | HG002complexvar | homalt | 99.1364 | 99.3080 | 98.9655 | 73.9209 | 287 | 2 | 287 | 3 | 2 | 66.6667 | |
| ckim-vqsr | INDEL | D16_PLUS | HG002complexvar | homalt | 98.7952 | 99.3080 | 98.2877 | 76.3371 | 287 | 2 | 287 | 5 | 4 | 80.0000 | |
| dgrover-gatk | INDEL | D16_PLUS | HG002complexvar | homalt | 98.7952 | 99.3080 | 98.2877 | 76.1047 | 287 | 2 | 287 | 5 | 4 | 80.0000 | |
| astatham-gatk | INDEL | D16_PLUS | HG002complexvar | homalt | 98.9655 | 99.3080 | 98.6254 | 76.4372 | 287 | 2 | 287 | 4 | 3 | 75.0000 | |
| bgallagher-sentieon | INDEL | D16_PLUS | HG002complexvar | homalt | 98.6254 | 99.3080 | 97.9522 | 76.0621 | 287 | 2 | 287 | 6 | 5 | 83.3333 | |
| bgallagher-sentieon | INDEL | D1_5 | map_l150_m0_e0 | * | 97.7917 | 99.3080 | 96.3211 | 91.7060 | 287 | 2 | 288 | 11 | 1 | 9.0909 | |
| ckim-dragen | INDEL | D16_PLUS | HG002complexvar | homalt | 95.9866 | 99.3080 | 92.8803 | 75.5924 | 287 | 2 | 287 | 22 | 20 | 90.9091 | |
| ckim-gatk | INDEL | D16_PLUS | HG002complexvar | homalt | 98.7952 | 99.3080 | 98.2877 | 76.3371 | 287 | 2 | 287 | 5 | 4 | 80.0000 | |
| astatham-gatk | SNP | * | map_l100_m1_e0 | homalt | 99.6081 | 99.3075 | 99.9106 | 57.8259 | 26816 | 187 | 26816 | 24 | 19 | 79.1667 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.5654 | 99.3064 | 99.8258 | 36.8073 | 1718 | 12 | 1719 | 3 | 3 | 100.0000 | |
| dgrover-gatk | SNP | ti | map_l125_m2_e0 | het | 99.2165 | 99.3060 | 99.1273 | 77.0589 | 18745 | 131 | 18741 | 165 | 34 | 20.6061 | |
| jlack-gatk | SNP | tv | map_l100_m1_e0 | het | 94.3447 | 99.3060 | 89.8556 | 80.1334 | 15310 | 107 | 15306 | 1728 | 90 | 5.2083 | |
| eyeh-varpipe | SNP | * | map_l250_m1_e0 | het | 98.4331 | 99.3060 | 97.5755 | 90.8816 | 4722 | 33 | 4588 | 114 | 8 | 7.0175 | |
| ghariani-varprowl | SNP | tv | map_l100_m1_e0 | het | 97.2713 | 99.3060 | 95.3184 | 75.1777 | 15310 | 107 | 15311 | 752 | 97 | 12.8989 | |
| ltrigg-rtg1 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 99.6201 | 99.3057 | 99.9365 | 31.9250 | 4720 | 33 | 4718 | 3 | 3 | 100.0000 | |
| ltrigg-rtg1 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 99.2905 | 99.3056 | 99.2754 | 83.8445 | 715 | 5 | 685 | 5 | 0 | 0.0000 | |
| gduggal-bwavard | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 90.1456 | 99.3056 | 82.5328 | 68.5151 | 572 | 4 | 567 | 120 | 100 | 83.3333 | |
| bgallagher-sentieon | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 99.3822 | 99.3056 | 99.4590 | 87.2487 | 1287 | 9 | 1287 | 7 | 6 | 85.7143 | |
| cchapple-custom | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.5931 | 99.3054 | 99.8825 | 45.7630 | 3431 | 24 | 3401 | 4 | 4 | 100.0000 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.4779 | 99.3048 | 99.6516 | 61.8182 | 857 | 6 | 858 | 3 | 2 | 66.6667 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.5356 | 99.3048 | 99.7674 | 61.5385 | 857 | 6 | 858 | 2 | 1 | 50.0000 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 97.7407 | 99.3048 | 96.2251 | 62.9649 | 2714 | 19 | 2702 | 106 | 102 | 96.2264 | |
| egarrison-hhga | SNP | tv | HG002compoundhet | hetalt | 99.5928 | 99.3039 | 99.8833 | 23.6185 | 856 | 6 | 856 | 1 | 1 | 100.0000 | |
| egarrison-hhga | SNP | * | HG002compoundhet | hetalt | 99.5928 | 99.3039 | 99.8833 | 23.6185 | 856 | 6 | 856 | 1 | 1 | 100.0000 | |
| ndellapenna-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.5243 | 99.3038 | 99.7457 | 47.7582 | 1569 | 11 | 1569 | 4 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | D16_PLUS | * | het | 97.8168 | 99.3036 | 96.3739 | 78.4222 | 3137 | 22 | 2897 | 109 | 66 | 60.5505 | |
| bgallagher-sentieon | INDEL | D16_PLUS | * | het | 97.5876 | 99.3036 | 95.9298 | 78.0298 | 3137 | 22 | 2899 | 123 | 76 | 61.7886 | |
| astatham-gatk | INDEL | D16_PLUS | * | het | 97.7337 | 99.3036 | 96.2126 | 78.4600 | 3137 | 22 | 2896 | 114 | 70 | 61.4035 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.3532 | 99.3035 | 99.4030 | 66.0014 | 998 | 7 | 999 | 6 | 3 | 50.0000 | |
| jli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.5016 | 99.3035 | 99.7006 | 63.3236 | 998 | 7 | 999 | 3 | 2 | 66.6667 | |
| hfeng-pmm1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 99.0489 | 99.3034 | 98.7958 | 56.9516 | 11404 | 80 | 11404 | 139 | 132 | 94.9640 | |
| ciseli-custom | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 96.7305 | 99.3032 | 94.2877 | 46.8635 | 6698 | 47 | 6685 | 405 | 129 | 31.8519 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.5692 | 99.3032 | 97.8460 | 72.1465 | 5558 | 39 | 5542 | 122 | 111 | 90.9836 | |
| ckim-dragen | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.9169 | 99.3027 | 98.5341 | 69.1612 | 4415 | 31 | 4369 | 65 | 62 | 95.3846 | |
| hfeng-pmm3 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 99.3719 | 99.3026 | 99.4413 | 55.9656 | 712 | 5 | 712 | 4 | 3 | 75.0000 | |
| gduggal-bwafb | SNP | ti | map_l100_m2_e1 | homalt | 99.5933 | 99.3025 | 99.8858 | 63.9101 | 18365 | 129 | 18365 | 21 | 13 | 61.9048 | |
| ckim-vqsr | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.6992 | 99.3022 | 98.1034 | 41.3093 | 7400 | 52 | 7397 | 143 | 1 | 0.6993 | |
| jmaeng-gatk | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.5459 | 99.3019 | 99.7911 | 49.8616 | 6686 | 47 | 6688 | 14 | 9 | 64.2857 | |
| ckim-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 99.4172 | 99.3015 | 99.5333 | 49.8126 | 4265 | 30 | 4265 | 20 | 3 | 15.0000 | |
| jli-custom | INDEL | * | * | het | 99.5119 | 99.3015 | 99.7232 | 58.0133 | 192777 | 1356 | 192389 | 534 | 340 | 63.6704 | |
| hfeng-pmm2 | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.6074 | 99.3012 | 99.9156 | 37.6986 | 10657 | 75 | 10657 | 9 | 0 | 0.0000 | |
| eyeh-varpipe | SNP | tv | map_l250_m0_e0 | het | 97.3196 | 99.3007 | 95.4160 | 94.4664 | 568 | 4 | 562 | 27 | 2 | 7.4074 | |
| jlack-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 97.8331 | 99.2999 | 96.4089 | 78.7770 | 28511 | 201 | 28511 | 1062 | 52 | 4.8964 | |
| jlack-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 97.8331 | 99.2999 | 96.4089 | 78.7770 | 28511 | 201 | 28511 | 1062 | 52 | 4.8964 | |
| jli-custom | SNP | * | map_l125_m0_e0 | homalt | 99.5817 | 99.2998 | 99.8651 | 65.5375 | 6665 | 47 | 6665 | 9 | 9 | 100.0000 | |
| ltrigg-rtg2 | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.5386 | 99.2998 | 99.7786 | 39.6095 | 2269 | 16 | 2253 | 5 | 1 | 20.0000 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 99.0393 | 99.2995 | 98.7805 | 65.9953 | 567 | 4 | 567 | 7 | 7 | 100.0000 | |