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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
24151-24200 / 86044 show all | |||||||||||||||
| gduggal-snapvard | SNP | * | map_l125_m2_e1 | het | 91.4989 | 96.9163 | 86.6551 | 82.4293 | 28726 | 914 | 28383 | 4371 | 310 | 7.0922 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.3304 | 96.9158 | 97.7485 | 53.9045 | 14329 | 456 | 14327 | 330 | 320 | 96.9697 | |
| jli-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 97.9085 | 96.9156 | 98.9221 | 57.0053 | 1194 | 38 | 1193 | 13 | 11 | 84.6154 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 97.3004 | 96.9154 | 97.6884 | 63.0249 | 974 | 31 | 972 | 23 | 16 | 69.5652 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.2911 | 96.9146 | 97.6705 | 52.3019 | 35463 | 1129 | 35387 | 844 | 761 | 90.1659 | |
| mlin-fermikit | INDEL | D1_5 | HG002complexvar | homalt | 96.1786 | 96.9145 | 95.4537 | 57.9255 | 10271 | 327 | 10183 | 485 | 469 | 96.7010 | |
| rpoplin-dv42 | INDEL | I1_5 | map_l125_m1_e0 | het | 98.1263 | 96.9136 | 99.3697 | 85.6928 | 471 | 15 | 473 | 3 | 2 | 66.6667 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 96.6125 | 96.9110 | 96.3159 | 71.1607 | 3451 | 110 | 3451 | 132 | 77 | 58.3333 | |
| asubramanian-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.4262 | 96.9096 | 99.9911 | 63.7599 | 11195 | 357 | 11199 | 1 | 1 | 100.0000 | |
| asubramanian-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.4262 | 96.9096 | 99.9911 | 63.7599 | 11195 | 357 | 11199 | 1 | 1 | 100.0000 | |
| ltrigg-rtg1 | INDEL | * | map_siren | * | 97.9785 | 96.9096 | 99.0713 | 78.1949 | 7181 | 229 | 7147 | 67 | 16 | 23.8806 | |
| ndellapenna-hhga | INDEL | * | map_l150_m2_e0 | het | 97.4002 | 96.9095 | 97.8959 | 89.3401 | 878 | 28 | 884 | 19 | 5 | 26.3158 | |
| rpoplin-dv42 | INDEL | * | map_l125_m2_e0 | het | 97.6481 | 96.9087 | 98.3988 | 86.9392 | 1348 | 43 | 1352 | 22 | 7 | 31.8182 | |
| gduggal-bwafb | SNP | * | map_l250_m1_e0 | het | 97.0310 | 96.9085 | 97.1537 | 89.8249 | 4608 | 147 | 4608 | 135 | 33 | 24.4444 | |
| qzeng-custom | INDEL | D1_5 | HG002compoundhet | homalt | 77.4248 | 96.9072 | 64.4647 | 67.2143 | 282 | 9 | 283 | 156 | 151 | 96.7949 | |
| qzeng-custom | SNP | ti | * | hetalt | 98.0808 | 96.9072 | 99.2832 | 55.8893 | 564 | 18 | 554 | 4 | 4 | 100.0000 | |
| egarrison-hhga | SNP | tv | map_l250_m2_e0 | het | 98.0955 | 96.9072 | 99.3133 | 87.4569 | 1880 | 60 | 1880 | 13 | 5 | 38.4615 | |
| eyeh-varpipe | INDEL | D1_5 | HG002compoundhet | homalt | 11.1474 | 96.9072 | 5.9138 | 65.1721 | 282 | 9 | 243 | 3866 | 3861 | 99.8707 | |
| ckim-dragen | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_51to200 | hetalt | 98.4293 | 96.9072 | 100.0000 | 20.3390 | 94 | 3 | 94 | 0 | 0 | ||
| ltrigg-rtg2 | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 98.1282 | 96.9069 | 99.3807 | 45.7062 | 10151 | 324 | 10430 | 65 | 64 | 98.4615 | |
| astatham-gatk | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 95.4126 | 96.9059 | 93.9646 | 79.4691 | 3915 | 125 | 3612 | 232 | 195 | 84.0517 | |
| cchapple-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.9495 | 96.9056 | 99.0161 | 33.0779 | 17694 | 565 | 18416 | 183 | 178 | 97.2678 | |
| ckim-vqsr | INDEL | I1_5 | map_siren | * | 98.0317 | 96.9052 | 99.1848 | 83.6671 | 2912 | 93 | 2920 | 24 | 8 | 33.3333 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 97.6568 | 96.9051 | 98.4202 | 76.2358 | 1910 | 61 | 1869 | 30 | 19 | 63.3333 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 97.6568 | 96.9051 | 98.4202 | 76.2358 | 1910 | 61 | 1869 | 30 | 19 | 63.3333 | |
| gduggal-bwavard | SNP | tv | HG002complexvar | homalt | 98.3914 | 96.9047 | 99.9244 | 20.9085 | 92167 | 2944 | 89912 | 68 | 35 | 51.4706 | |
| ciseli-custom | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 83.4518 | 96.9037 | 73.2793 | 50.2099 | 11079 | 354 | 11126 | 4057 | 61 | 1.5036 | |
| ckim-dragen | INDEL | * | map_l125_m2_e0 | * | 96.6158 | 96.9035 | 96.3299 | 89.2603 | 2128 | 68 | 2126 | 81 | 13 | 16.0494 | |
| anovak-vg | SNP | tv | HG002complexvar | het | 97.4369 | 96.9012 | 97.9786 | 22.5474 | 146063 | 4671 | 144347 | 2978 | 2196 | 73.7408 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 98.0428 | 96.9002 | 99.2126 | 71.4874 | 1563 | 50 | 1512 | 12 | 7 | 58.3333 | |
| ckim-dragen | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.1935 | 96.8999 | 97.4889 | 57.0530 | 36727 | 1175 | 36532 | 941 | 927 | 98.5122 | |
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.0631 | 96.8992 | 99.2554 | 50.7827 | 31000 | 992 | 30924 | 232 | 217 | 93.5345 | |
| gduggal-bwafb | INDEL | I1_5 | * | * | 97.8814 | 96.8991 | 98.8838 | 56.3942 | 145992 | 4672 | 146789 | 1657 | 1400 | 84.4900 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.7831 | 96.8990 | 98.6834 | 73.3610 | 62433 | 1998 | 63262 | 844 | 717 | 84.9526 | |
| ckim-dragen | INDEL | * | map_l125_m2_e1 | * | 96.5933 | 96.8989 | 96.2897 | 89.3425 | 2156 | 69 | 2154 | 83 | 14 | 16.8675 | |
| ciseli-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 82.4034 | 96.8987 | 71.6806 | 60.7006 | 1531 | 49 | 1544 | 610 | 3 | 0.4918 | |
| gduggal-snapvard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 88.6006 | 96.8987 | 81.6117 | 67.2685 | 1531 | 49 | 1509 | 340 | 6 | 1.7647 | |
| hfeng-pmm2 | INDEL | I6_15 | * | * | 97.8481 | 96.8980 | 98.8171 | 51.0141 | 24053 | 770 | 24058 | 288 | 265 | 92.0139 | |
| gduggal-bwavard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.4241 | 96.8972 | 100.0000 | 48.3349 | 1093 | 35 | 1086 | 0 | 0 | ||
| egarrison-hhga | SNP | tv | HG002compoundhet | het | 98.2001 | 96.8971 | 99.5386 | 52.4849 | 4528 | 145 | 4530 | 21 | 10 | 47.6190 | |
| ltrigg-rtg2 | INDEL | I1_5 | map_l125_m2_e1 | * | 97.9652 | 96.8966 | 99.0577 | 82.2719 | 843 | 27 | 841 | 8 | 0 | 0.0000 | |
| gduggal-snapfb | INDEL | I1_5 | map_l125_m2_e1 | * | 96.3932 | 96.8966 | 95.8951 | 88.3455 | 843 | 27 | 841 | 36 | 7 | 19.4444 | |
| gduggal-snapvard | SNP | tv | map_l125_m2_e1 | * | 93.1692 | 96.8962 | 89.7183 | 79.8287 | 16140 | 517 | 16082 | 1843 | 125 | 6.7824 | |
| gduggal-snapfb | SNP | * | map_l125_m1_e0 | * | 96.8640 | 96.8959 | 96.8321 | 72.7854 | 43920 | 1407 | 43924 | 1437 | 620 | 43.1454 | |
| raldana-dualsentieon | SNP | tv | map_l250_m2_e1 | het | 97.4661 | 96.8957 | 98.0433 | 89.2902 | 1904 | 61 | 1904 | 38 | 1 | 2.6316 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 82.1053 | 96.8944 | 71.2329 | 36.7052 | 156 | 5 | 156 | 63 | 63 | 100.0000 | |
| cchapple-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 84.9390 | 96.8944 | 75.6098 | 24.9084 | 156 | 5 | 155 | 50 | 50 | 100.0000 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.6760 | 96.8929 | 98.4720 | 68.6413 | 15093 | 484 | 15080 | 234 | 134 | 57.2650 | |
| gduggal-snapvard | SNP | ti | HG002complexvar | het | 97.7415 | 96.8929 | 98.6052 | 20.9330 | 304985 | 9780 | 300448 | 4250 | 1602 | 37.6941 | |
| gduggal-snapvard | SNP | * | map_l125_m2_e0 | het | 91.4436 | 96.8927 | 86.5748 | 82.3864 | 28407 | 911 | 28071 | 4353 | 308 | 7.0756 | |