PrecisionFDA
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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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
9201-9250 / 86044 show all | |||||||||||||||
| jmaeng-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.8269 | 98.7352 | 98.9188 | 69.0820 | 13583 | 174 | 13540 | 148 | 116 | 78.3784 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.8269 | 98.7352 | 98.9188 | 69.0820 | 13583 | 174 | 13540 | 148 | 116 | 78.3784 | |
| ltrigg-rtg1 | SNP | tv | map_siren | * | 99.4402 | 99.2053 | 99.6762 | 52.0914 | 45565 | 365 | 45564 | 148 | 13 | 8.7838 | |
| jli-custom | SNP | tv | map_siren | * | 99.6133 | 99.5493 | 99.6773 | 55.0835 | 45723 | 207 | 45718 | 148 | 36 | 24.3243 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 94.7579 | 92.9553 | 96.6318 | 48.7341 | 3246 | 246 | 4246 | 148 | 137 | 92.5676 | |
| anovak-vg | INDEL | C1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 23.5714 | 33.3333 | 18.2320 | 88.4787 | 1 | 2 | 33 | 148 | 6 | 4.0541 | |
| anovak-vg | INDEL | D1_5 | map_l150_m1_e0 | het | 80.6909 | 87.9668 | 74.5267 | 89.8052 | 424 | 58 | 433 | 148 | 55 | 37.1622 | |
| bgallagher-sentieon | SNP | * | map_l250_m2_e0 | * | 98.4835 | 98.8332 | 98.1363 | 89.4731 | 7793 | 92 | 7793 | 148 | 32 | 21.6216 | |
| asubramanian-gatk | INDEL | * | HG002complexvar | homalt | 99.4823 | 99.5116 | 99.4530 | 57.3903 | 26895 | 132 | 26910 | 148 | 101 | 68.2432 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 93.3705 | 92.2714 | 94.4961 | 50.6515 | 2543 | 213 | 2541 | 148 | 144 | 97.2973 | |
| hfeng-pmm3 | SNP | ti | map_siren | * | 99.7701 | 99.6881 | 99.8523 | 52.8057 | 100042 | 313 | 100027 | 148 | 25 | 16.8919 | |
| hfeng-pmm2 | SNP | ti | map_l150_m2_e0 | het | 99.0233 | 99.1926 | 98.8546 | 79.5912 | 12777 | 104 | 12773 | 148 | 13 | 8.7838 | |
| jlack-gatk | INDEL | D16_PLUS | HG002compoundhet | * | 92.8541 | 92.1401 | 93.5792 | 35.3980 | 2157 | 184 | 2157 | 148 | 143 | 96.6216 | |
| jlack-gatk | SNP | ti | func_cds | * | 99.4443 | 99.9565 | 98.9373 | 29.0994 | 13781 | 6 | 13779 | 148 | 1 | 0.6757 | |
| jlack-gatk | SNP | ti | func_cds | het | 99.1254 | 99.9765 | 98.2886 | 33.6861 | 8502 | 2 | 8500 | 148 | 1 | 0.6757 | |
| ghariani-varprowl | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 95.1742 | 99.7330 | 91.0140 | 84.2317 | 1494 | 4 | 1499 | 148 | 98 | 66.2162 | |
| hfeng-pmm1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 97.6041 | 96.4619 | 98.7737 | 60.3970 | 12078 | 443 | 11921 | 148 | 125 | 84.4595 | |
| ghariani-varprowl | INDEL | D1_5 | map_l125_m2_e1 | * | 91.8807 | 95.8513 | 88.2259 | 89.6373 | 1109 | 48 | 1109 | 148 | 28 | 18.9189 | |
| gduggal-snapvard | INDEL | C1_5 | map_siren | * | 0.0000 | 0.0000 | 45.1852 | 95.1587 | 0 | 0 | 122 | 148 | 16 | 10.8108 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 87.8840 | 90.4959 | 85.4187 | 61.0813 | 876 | 92 | 867 | 148 | 71 | 47.9730 | |
| ciseli-custom | SNP | tv | map_l250_m1_e0 | homalt | 77.9222 | 74.8832 | 81.2183 | 87.6682 | 641 | 215 | 640 | 148 | 105 | 70.9459 | |
| ckim-dragen | SNP | tv | HG002complexvar | het | 99.9058 | 99.9098 | 99.9019 | 22.2740 | 150595 | 136 | 150740 | 148 | 70 | 47.2973 | |
| ckim-gatk | INDEL | * | map_l100_m1_e0 | het | 96.1061 | 98.6130 | 93.7235 | 89.8156 | 2204 | 31 | 2210 | 148 | 14 | 9.4595 | |
| ckim-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.1889 | 97.3395 | 97.0388 | 75.6563 | 4866 | 133 | 4850 | 148 | 106 | 71.6216 | |
| ckim-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.1889 | 97.3395 | 97.0388 | 75.6563 | 4866 | 133 | 4850 | 148 | 106 | 71.6216 | |
| ckim-vqsr | SNP | ti | map_l125_m1_e0 | het | 81.0388 | 68.6740 | 98.8337 | 87.9988 | 12544 | 5722 | 12542 | 148 | 2 | 1.3514 | |
| egarrison-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 77.6152 | 64.0108 | 98.5632 | 45.9265 | 10693 | 6012 | 10153 | 148 | 131 | 88.5135 | |
| egarrison-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 77.6152 | 64.0108 | 98.5632 | 45.9265 | 10693 | 6012 | 10153 | 148 | 131 | 88.5135 | |
| egarrison-hhga | SNP | * | map_siren | het | 99.5365 | 99.2384 | 99.8364 | 54.0342 | 90298 | 693 | 90299 | 148 | 53 | 35.8108 | |
| rpoplin-dv42 | SNP | ti | map_l125_m2_e0 | * | 99.3062 | 99.1044 | 99.5088 | 70.7721 | 29987 | 271 | 29983 | 148 | 102 | 68.9189 | |
| rpoplin-dv42 | SNP | ti | map_l125_m2_e1 | * | 99.3100 | 99.1069 | 99.5138 | 70.8133 | 30296 | 273 | 30292 | 148 | 102 | 68.9189 | |
| raldana-dualsentieon | INDEL | D6_15 | * | homalt | 98.7805 | 99.8735 | 97.7111 | 54.0245 | 6318 | 8 | 6318 | 148 | 145 | 97.9730 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 97.9932 | 99.8407 | 96.2129 | 58.2077 | 3760 | 6 | 3760 | 148 | 145 | 97.9730 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 97.9932 | 99.8407 | 96.2129 | 58.2077 | 3760 | 6 | 3760 | 148 | 145 | 97.9730 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 91.2102 | 88.3164 | 94.3001 | 47.2057 | 2434 | 322 | 2432 | 147 | 146 | 99.3197 | |
| rpoplin-dv42 | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.9893 | 96.9635 | 99.0370 | 71.9042 | 15104 | 473 | 15118 | 147 | 133 | 90.4762 | |
| rpoplin-dv42 | SNP | ti | map_l125_m1_e0 | * | 99.2894 | 99.0830 | 99.4967 | 68.8733 | 29066 | 269 | 29062 | 147 | 101 | 68.7075 | |
| hfeng-pmm1 | SNP | * | map_l125_m2_e1 | * | 99.4713 | 99.2564 | 99.6872 | 70.6981 | 46851 | 351 | 46845 | 147 | 41 | 27.8912 | |
| jpowers-varprowl | INDEL | D1_5 | map_siren | het | 95.3594 | 97.0136 | 93.7606 | 83.6842 | 2209 | 68 | 2209 | 147 | 108 | 73.4694 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 87.7292 | 95.8398 | 80.8843 | 58.8109 | 622 | 27 | 622 | 147 | 141 | 95.9184 | |
| ndellapenna-hhga | INDEL | * | HG002compoundhet | hetalt | 85.1313 | 74.5631 | 99.1899 | 56.3007 | 18775 | 6405 | 18000 | 147 | 122 | 82.9932 | |
| gduggal-bwavard | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | het | 97.4259 | 97.9953 | 96.8630 | 51.4454 | 4595 | 94 | 4539 | 147 | 42 | 28.5714 | |
| gduggal-snapfb | INDEL | * | map_l100_m1_e0 | * | 93.4753 | 91.3274 | 95.7267 | 83.9230 | 3275 | 311 | 3293 | 147 | 38 | 25.8503 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 92.5216 | 89.4845 | 95.7722 | 64.1176 | 3489 | 410 | 3330 | 147 | 104 | 70.7483 | |
| gduggal-bwafb | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 79.4509 | 70.3322 | 91.2863 | 53.7682 | 2456 | 1036 | 1540 | 147 | 142 | 96.5986 | |
| gduggal-bwafb | SNP | ti | map_l125_m0_e0 | * | 98.6735 | 98.5034 | 98.8442 | 76.2289 | 12571 | 191 | 12571 | 147 | 47 | 31.9728 | |
| astatham-gatk | INDEL | D1_5 | HG002compoundhet | homalt | 79.6703 | 99.6564 | 66.3616 | 87.7109 | 290 | 1 | 290 | 147 | 146 | 99.3197 | |
| bgallagher-sentieon | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | het | 76.6399 | 92.0408 | 65.6542 | 80.0373 | 451 | 39 | 281 | 147 | 142 | 96.5986 | |
| astatham-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 93.6375 | 98.9848 | 88.8383 | 60.2115 | 1170 | 12 | 1170 | 147 | 145 | 98.6395 | |
| anovak-vg | INDEL | C1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 21.1765 | 33.3333 | 15.5172 | 87.3085 | 1 | 2 | 27 | 147 | 5 | 3.4014 | |