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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
19851-19900 / 86044 show all | |||||||||||||||
| ckim-dragen | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 98.8470 | 98.2089 | 99.4934 | 48.2524 | 2906 | 53 | 2946 | 15 | 4 | 26.6667 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 84.5989 | 77.2532 | 93.4884 | 70.0139 | 180 | 53 | 201 | 14 | 12 | 85.7143 | |
| ckim-isaac | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 63.5631 | 57.2581 | 71.4286 | 99.8537 | 71 | 53 | 65 | 26 | 10 | 38.4615 | |
| ckim-isaac | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | * | 81.9633 | 76.1261 | 88.7701 | 48.1994 | 169 | 53 | 166 | 21 | 16 | 76.1905 | |
| asubramanian-gatk | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | * | 99.1035 | 98.9086 | 99.2991 | 66.9100 | 4803 | 53 | 4817 | 34 | 12 | 35.2941 | |
| anovak-vg | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 95.6073 | 97.0006 | 94.2535 | 58.3072 | 1714 | 53 | 1755 | 107 | 94 | 87.8505 | |
| astatham-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.5583 | 99.5229 | 99.5937 | 62.9090 | 11055 | 53 | 11030 | 45 | 18 | 40.0000 | |
| astatham-gatk | INDEL | * | map_l150_m1_e0 | * | 96.6569 | 96.0389 | 97.2830 | 90.5512 | 1285 | 53 | 1289 | 36 | 7 | 19.4444 | |
| astatham-gatk | INDEL | * | map_l150_m2_e0 | het | 95.2620 | 94.1501 | 96.4004 | 91.7487 | 853 | 53 | 857 | 32 | 4 | 12.5000 | |
| astatham-gatk | INDEL | I1_5 | map_l125_m2_e0 | * | 96.2887 | 93.8156 | 98.8957 | 87.9420 | 804 | 53 | 806 | 9 | 2 | 22.2222 | |
| astatham-gatk | INDEL | I1_5 | map_l125_m2_e0 | het | 93.7725 | 89.3360 | 98.6726 | 89.3947 | 444 | 53 | 446 | 6 | 0 | 0.0000 | |
| asubramanian-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 98.5454 | 98.2333 | 98.8594 | 76.8466 | 2947 | 53 | 2947 | 34 | 5 | 14.7059 | |
| asubramanian-gatk | INDEL | * | map_l125_m2_e0 | homalt | 96.2060 | 93.0537 | 99.5792 | 87.7027 | 710 | 53 | 710 | 3 | 1 | 33.3333 | |
| asubramanian-gatk | INDEL | * | map_l150_m0_e0 | * | 90.5945 | 89.6887 | 91.5187 | 98.1956 | 461 | 53 | 464 | 43 | 3 | 6.9767 | |
| asubramanian-gatk | INDEL | * | map_l250_m2_e1 | * | 86.7031 | 84.0841 | 89.4904 | 99.1381 | 280 | 53 | 281 | 33 | 3 | 9.0909 | |
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 93.6047 | 90.1119 | 97.3790 | 63.5026 | 483 | 53 | 483 | 13 | 11 | 84.6154 | |
| anovak-vg | INDEL | D6_15 | map_l100_m1_e0 | hetalt | 0.0000 | 22.0588 | 0.0000 | 0.0000 | 15 | 53 | 0 | 0 | 0 | ||
| anovak-vg | INDEL | D6_15 | map_l100_m2_e0 | hetalt | 0.0000 | 22.0588 | 0.0000 | 0.0000 | 15 | 53 | 0 | 0 | 0 | ||
| ltrigg-rtg1 | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.8164 | 99.6914 | 99.9417 | 52.6220 | 17124 | 53 | 17138 | 10 | 7 | 70.0000 | |
| jmaeng-gatk | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.4801 | 99.6983 | 99.2628 | 67.4240 | 17515 | 53 | 17505 | 130 | 11 | 8.4615 | |
| jpowers-varprowl | INDEL | * | map_l125_m2_e1 | homalt | 95.9415 | 93.1525 | 98.9026 | 83.4356 | 721 | 53 | 721 | 8 | 5 | 62.5000 | |
| ltrigg-rtg1 | INDEL | * | segdup | * | 98.6010 | 97.9264 | 99.2849 | 92.9892 | 2503 | 53 | 2499 | 18 | 5 | 27.7778 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 91.1412 | 85.3591 | 97.7636 | 73.7636 | 309 | 53 | 306 | 7 | 7 | 100.0000 | |
| ltrigg-rtg1 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 98.9025 | 98.1098 | 99.7081 | 39.8904 | 2751 | 53 | 2733 | 8 | 8 | 100.0000 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 96.6173 | 96.2411 | 96.9963 | 75.2089 | 1357 | 53 | 1324 | 41 | 35 | 85.3659 | |
| jmaeng-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 97.3197 | 98.8079 | 95.8756 | 69.0152 | 4393 | 53 | 4347 | 187 | 182 | 97.3262 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 95.4096 | 96.1426 | 94.6877 | 69.8615 | 1321 | 53 | 1319 | 74 | 68 | 91.8919 | |
| jpowers-varprowl | SNP | tv | map_l150_m0_e0 | homalt | 97.6637 | 96.0090 | 99.3765 | 82.5845 | 1275 | 53 | 1275 | 8 | 2 | 25.0000 | |
| raldana-dualsentieon | SNP | ti | HG002complexvar | homalt | 99.9811 | 99.9726 | 99.9897 | 18.3281 | 193410 | 53 | 193401 | 20 | 20 | 100.0000 | |
| raldana-dualsentieon | SNP | ti | map_l100_m1_e0 | homalt | 99.8161 | 99.7049 | 99.9275 | 56.2318 | 17907 | 53 | 17907 | 13 | 12 | 92.3077 | |
| raldana-dualsentieon | SNP | ti | map_l100_m2_e0 | homalt | 99.8196 | 99.7105 | 99.9288 | 58.8267 | 18256 | 53 | 18256 | 13 | 12 | 92.3077 | |
| raldana-dualsentieon | SNP | ti | map_l100_m2_e1 | homalt | 99.8214 | 99.7134 | 99.9296 | 58.8080 | 18441 | 53 | 18441 | 13 | 12 | 92.3077 | |
| rpoplin-dv42 | INDEL | * | map_l125_m2_e1 | * | 98.0600 | 97.6180 | 98.5061 | 98.7184 | 2172 | 53 | 2176 | 33 | 14 | 42.4242 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 89.0411 | 92.8475 | 85.5346 | 72.4341 | 688 | 53 | 680 | 115 | 105 | 91.3043 | |
| raldana-dualsentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 91.5664 | 93.9498 | 89.3010 | 79.9025 | 823 | 53 | 626 | 75 | 74 | 98.6667 | |
| raldana-dualsentieon | INDEL | D6_15 | HG002complexvar | hetalt | 97.2668 | 94.7680 | 99.9010 | 47.1204 | 960 | 53 | 1009 | 1 | 1 | 100.0000 | |
| raldana-dualsentieon | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 88.8446 | 80.7971 | 98.6726 | 90.8055 | 223 | 53 | 223 | 3 | 1 | 33.3333 | |
| eyeh-varpipe | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 49.3293 | 79.5367 | 35.7513 | 30.4087 | 206 | 53 | 207 | 372 | 357 | 95.9677 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 67.1072 | 91.8336 | 52.8714 | 33.4573 | 596 | 53 | 3121 | 2782 | 2751 | 98.8857 | |
| eyeh-varpipe | INDEL | I1_5 | map_l100_m2_e0 | * | 96.3034 | 96.1257 | 96.4817 | 82.0384 | 1315 | 53 | 2139 | 78 | 60 | 76.9231 | |
| gduggal-bwafb | INDEL | I16_PLUS | HG002complexvar | homalt | 87.0748 | 82.8479 | 91.7563 | 38.8158 | 256 | 53 | 256 | 23 | 22 | 95.6522 | |
| gduggal-bwafb | INDEL | I16_PLUS | map_siren | * | 54.1375 | 38.3721 | 91.8919 | 72.3881 | 33 | 53 | 34 | 3 | 3 | 100.0000 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 79.0727 | 65.8065 | 99.0385 | 90.3435 | 102 | 53 | 103 | 1 | 0 | 0.0000 | |
| gduggal-bwaplat | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 32.9114 | 19.6970 | 100.0000 | 90.5109 | 13 | 53 | 13 | 0 | 0 | ||
| gduggal-bwavard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 96.3297 | 97.9167 | 94.7933 | 63.6617 | 2491 | 53 | 2476 | 136 | 15 | 11.0294 | |
| gduggal-bwavard | SNP | tv | map_l150_m0_e0 | het | 87.7034 | 98.1358 | 79.2759 | 87.9471 | 2790 | 53 | 2781 | 727 | 17 | 2.3384 | |
| gduggal-snapfb | INDEL | * | map_l125_m0_e0 | het | 91.8622 | 90.9710 | 92.7711 | 85.6224 | 534 | 53 | 539 | 42 | 9 | 21.4286 | |
| eyeh-varpipe | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 87.1597 | 96.2729 | 79.6226 | 85.7802 | 1369 | 53 | 1055 | 270 | 36 | 13.3333 | |
| dgrover-gatk | SNP | * | map_l250_m0_e0 | * | 97.6090 | 97.5176 | 97.7006 | 93.8613 | 2082 | 53 | 2082 | 49 | 10 | 20.4082 | |
| dgrover-gatk | SNP | tv | map_l100_m0_e0 | het | 98.8895 | 99.2661 | 98.5157 | 76.1747 | 7169 | 53 | 7168 | 108 | 20 | 18.5185 | |