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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
26851-26900 / 86044 show all | |||||||||||||||
| ckim-dragen | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 97.2603 | 95.9459 | 98.6111 | 80.6971 | 71 | 3 | 71 | 1 | 1 | 100.0000 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 97.2603 | 95.9459 | 98.6111 | 81.3953 | 71 | 3 | 71 | 1 | 1 | 100.0000 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 97.2603 | 95.9459 | 98.6111 | 80.4878 | 71 | 3 | 71 | 1 | 1 | 100.0000 | |
| gduggal-snapplat | SNP | ti | HG002complexvar | * | 98.2167 | 97.8257 | 98.6108 | 20.9389 | 497382 | 11055 | 497799 | 7013 | 1203 | 17.1539 | |
| ltrigg-rtg1 | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.0496 | 99.4927 | 98.6105 | 40.0631 | 11375 | 58 | 11426 | 161 | 2 | 1.2422 | |
| ckim-vqsr | SNP | * | map_l125_m1_e0 | het | 80.8165 | 68.4629 | 98.6098 | 88.4760 | 19438 | 8954 | 19435 | 274 | 3 | 1.0949 | |
| raldana-dualsentieon | INDEL | D1_5 | map_l125_m1_e0 | * | 98.1075 | 97.6103 | 98.6098 | 84.5171 | 1062 | 26 | 1064 | 15 | 4 | 26.6667 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.9346 | 99.2616 | 98.6098 | 64.3360 | 8334 | 62 | 8299 | 117 | 105 | 89.7436 | |
| gduggal-bwafb | SNP | tv | map_l100_m2_e0 | * | 98.8866 | 99.1651 | 98.6097 | 70.4745 | 24824 | 209 | 24824 | 350 | 55 | 15.7143 | |
| ckim-vqsr | SNP | ti | map_l150_m2_e0 | het | 78.3377 | 64.9794 | 98.6095 | 91.3777 | 8370 | 4511 | 8368 | 118 | 2 | 1.6949 | |
| egarrison-hhga | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 80.7503 | 68.3682 | 98.6094 | 40.8377 | 817 | 378 | 780 | 11 | 9 | 81.8182 | |
| rpoplin-dv42 | SNP | tv | map_l125_m0_e0 | * | 98.4900 | 98.3713 | 98.6090 | 73.3113 | 6523 | 108 | 6522 | 92 | 52 | 56.5217 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 94.6607 | 91.0166 | 98.6088 | 31.6968 | 6079 | 600 | 5954 | 84 | 72 | 85.7143 | |
| ltrigg-rtg1 | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 96.9514 | 95.3488 | 98.6087 | 46.3119 | 574 | 28 | 567 | 8 | 6 | 75.0000 | |
| jlack-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 98.8694 | 99.1317 | 98.6084 | 82.6759 | 4110 | 36 | 4110 | 58 | 16 | 27.5862 | |
| raldana-dualsentieon | SNP | * | map_l125_m2_e1 | het | 98.7960 | 98.9845 | 98.6083 | 74.0672 | 29339 | 301 | 29333 | 414 | 4 | 0.9662 | |
| gduggal-snapvard | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 97.1847 | 95.8015 | 98.6083 | 75.1972 | 502 | 22 | 496 | 7 | 4 | 57.1429 | |
| jli-custom | INDEL | * | map_l100_m1_e0 | het | 98.3638 | 98.1208 | 98.6080 | 83.1747 | 2193 | 42 | 2196 | 31 | 9 | 29.0323 | |
| ltrigg-rtg2 | SNP | * | segdup | * | 99.1371 | 99.6722 | 98.6078 | 87.3153 | 27975 | 92 | 27977 | 395 | 53 | 13.4177 | |
| rpoplin-dv42 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 96.3952 | 94.2799 | 98.6075 | 61.7292 | 7928 | 481 | 7931 | 112 | 102 | 91.0714 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 94.0239 | 89.8477 | 98.6072 | 53.8165 | 1062 | 120 | 1062 | 15 | 14 | 93.3333 | |
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 96.5336 | 94.5455 | 98.6072 | 76.2252 | 364 | 21 | 354 | 5 | 4 | 80.0000 | |
| mlin-fermikit | SNP | * | map_l100_m2_e0 | het | 71.6803 | 56.3051 | 98.6068 | 57.9033 | 26125 | 20274 | 26117 | 369 | 11 | 2.9810 | |
| jli-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 99.0815 | 99.5612 | 98.6064 | 70.5927 | 28586 | 126 | 28586 | 404 | 25 | 6.1881 | |
| jli-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 99.0815 | 99.5612 | 98.6064 | 70.5927 | 28586 | 126 | 28586 | 404 | 25 | 6.1881 | |
| egarrison-hhga | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 98.8929 | 99.1813 | 98.6063 | 58.3656 | 848 | 7 | 849 | 12 | 3 | 25.0000 | |
| mlin-fermikit | INDEL | I16_PLUS | HG002compoundhet | hetalt | 66.4170 | 50.0717 | 98.6059 | 45.0179 | 1048 | 1045 | 1061 | 15 | 14 | 93.3333 | |
| jli-custom | INDEL | * | map_l100_m2_e0 | het | 98.3050 | 98.0061 | 98.6057 | 84.0570 | 2261 | 46 | 2263 | 32 | 9 | 28.1250 | |
| hfeng-pmm1 | INDEL | I1_5 | map_l150_m1_e0 | * | 98.0147 | 97.4308 | 98.6056 | 88.2104 | 493 | 13 | 495 | 7 | 2 | 28.5714 | |
| gduggal-bwavard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 80.6406 | 68.2128 | 98.6056 | 59.6463 | 500 | 233 | 495 | 7 | 6 | 85.7143 | |
| gduggal-snapfb | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.1501 | 99.7008 | 98.6054 | 62.2072 | 6998 | 21 | 7000 | 99 | 15 | 15.1515 | |
| gduggal-snapvard | SNP | ti | HG002complexvar | het | 97.7415 | 96.8929 | 98.6052 | 20.9330 | 304985 | 9780 | 300448 | 4250 | 1602 | 37.6941 | |
| hfeng-pmm3 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 95.5521 | 92.6829 | 98.6047 | 87.0091 | 228 | 18 | 212 | 3 | 0 | 0.0000 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | het | 76.2290 | 62.1302 | 98.6047 | 43.8642 | 105 | 64 | 424 | 6 | 6 | 100.0000 | |
| gduggal-bwafb | SNP | tv | map_l100_m1_e0 | * | 98.8766 | 99.1511 | 98.6037 | 68.5198 | 24293 | 208 | 24293 | 344 | 55 | 15.9884 | |
| egarrison-hhga | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 79.2993 | 66.3164 | 98.6030 | 66.3016 | 10224 | 5193 | 9740 | 138 | 125 | 90.5797 | |
| dgrover-gatk | SNP | ti | map_l125_m0_e0 | het | 98.8408 | 99.0802 | 98.6026 | 80.1354 | 8187 | 76 | 8185 | 116 | 25 | 21.5517 | |
| jli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.9293 | 97.2651 | 98.6025 | 47.2860 | 13408 | 377 | 13406 | 190 | 185 | 97.3684 | |
| mlin-fermikit | SNP | * | map_l100_m2_e1 | het | 71.9034 | 56.5824 | 98.6024 | 57.9966 | 26536 | 20362 | 26528 | 376 | 11 | 2.9255 | |
| bgallagher-sentieon | SNP | tv | map_l150_m2_e0 | * | 98.9822 | 99.3659 | 98.6015 | 77.4624 | 11283 | 72 | 11281 | 160 | 25 | 15.6250 | |
| mlin-fermikit | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 98.1429 | 97.6886 | 98.6014 | 32.5284 | 7185 | 170 | 7191 | 102 | 76 | 74.5098 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 84.0126 | 73.1844 | 98.6014 | 27.7778 | 131 | 48 | 141 | 2 | 1 | 50.0000 | |
| ckim-vqsr | INDEL | * | map_l125_m0_e0 | homalt | 98.9474 | 99.2958 | 98.6014 | 88.7224 | 282 | 2 | 282 | 4 | 3 | 75.0000 | |
| ckim-vqsr | SNP | tv | map_l125_m2_e1 | * | 69.8938 | 54.1334 | 98.6002 | 89.6003 | 9017 | 7640 | 9016 | 128 | 1 | 0.7813 | |
| ghariani-varprowl | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.2514 | 99.9113 | 98.6002 | 57.2710 | 1127 | 1 | 1127 | 16 | 10 | 62.5000 | |
| ckim-dragen | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.6571 | 96.7320 | 98.6000 | 85.4100 | 1480 | 50 | 1479 | 21 | 15 | 71.4286 | |
| ckim-dragen | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.6571 | 96.7320 | 98.6000 | 85.4100 | 1480 | 50 | 1479 | 21 | 15 | 71.4286 | |
| jli-custom | INDEL | D6_15 | map_siren | * | 97.7205 | 96.8566 | 98.6000 | 82.0660 | 493 | 16 | 493 | 7 | 1 | 14.2857 | |
| raldana-dualsentieon | INDEL | D1_5 | map_l100_m0_e0 | * | 98.1974 | 97.7984 | 98.5998 | 82.9317 | 844 | 19 | 845 | 12 | 3 | 25.0000 | |
| cchapple-custom | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.0126 | 97.4325 | 98.5996 | 53.5616 | 15635 | 412 | 16687 | 237 | 217 | 91.5612 | |