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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
27301-27350 / 86044 show all | |||||||||||||||
| gduggal-snapfb | SNP | ti | HG002complexvar | het | 99.0494 | 99.5771 | 98.5273 | 20.1517 | 313435 | 1331 | 313897 | 4692 | 557 | 11.8713 | |
| jli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 96.2429 | 94.0621 | 98.5272 | 72.0921 | 697 | 44 | 669 | 10 | 8 | 80.0000 | |
| eyeh-varpipe | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.8642 | 99.2036 | 98.5271 | 69.1157 | 11460 | 92 | 11104 | 166 | 51 | 30.7229 | |
| eyeh-varpipe | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.8642 | 99.2036 | 98.5271 | 69.1157 | 11460 | 92 | 11104 | 166 | 51 | 30.7229 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.8574 | 99.1901 | 98.5270 | 64.5573 | 8328 | 68 | 8294 | 124 | 111 | 89.5161 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 98.8560 | 99.1874 | 98.5268 | 58.9697 | 7324 | 60 | 7290 | 109 | 104 | 95.4128 | |
| jli-custom | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 95.9552 | 93.5145 | 98.5267 | 75.6611 | 1067 | 74 | 1070 | 16 | 10 | 62.5000 | |
| dgrover-gatk | SNP | * | map_l250_m2_e0 | * | 98.4387 | 98.3513 | 98.5262 | 90.2982 | 7755 | 130 | 7755 | 116 | 30 | 25.8621 | |
| astatham-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.2824 | 98.0398 | 98.5261 | 67.2886 | 64070 | 1281 | 63840 | 955 | 849 | 88.9005 | |
| astatham-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.2824 | 98.0398 | 98.5261 | 67.2886 | 64070 | 1281 | 63840 | 955 | 849 | 88.9005 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 92.9204 | 87.9187 | 98.5255 | 66.5471 | 735 | 101 | 735 | 11 | 9 | 81.8182 | |
| jpowers-varprowl | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 98.8896 | 99.2565 | 98.5255 | 64.2421 | 2937 | 22 | 2940 | 44 | 10 | 22.7273 | |
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.1165 | 95.7477 | 98.5251 | 68.8562 | 5359 | 238 | 5344 | 80 | 71 | 88.7500 | |
| hfeng-pmm2 | SNP | tv | map_l150_m2_e1 | het | 98.8125 | 99.1018 | 98.5248 | 79.6036 | 7282 | 66 | 7280 | 109 | 10 | 9.1743 | |
| astatham-gatk | INDEL | I6_15 | * | * | 97.8089 | 97.1035 | 98.5247 | 52.8353 | 24104 | 719 | 24109 | 361 | 337 | 93.3518 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 81.8581 | 70.0143 | 98.5246 | 47.8186 | 488 | 209 | 601 | 9 | 7 | 77.7778 | |
| ckim-dragen | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.2565 | 100.0000 | 98.5240 | 66.2935 | 267 | 0 | 267 | 4 | 4 | 100.0000 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 78.4355 | 65.1515 | 98.5240 | 37.7011 | 301 | 161 | 267 | 4 | 3 | 75.0000 | |
| ckim-dragen | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.8131 | 97.1129 | 98.5235 | 67.3246 | 740 | 22 | 734 | 11 | 10 | 90.9091 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.4121 | 96.3255 | 98.5235 | 67.0062 | 734 | 28 | 734 | 11 | 7 | 63.6364 | |
| gduggal-bwafb | INDEL | D6_15 | HG002complexvar | het | 93.9461 | 89.7756 | 98.5230 | 50.1907 | 2801 | 319 | 3602 | 54 | 30 | 55.5556 | |
| ckim-isaac | INDEL | * | map_l150_m2_e1 | * | 74.8271 | 60.3197 | 98.5227 | 91.3700 | 868 | 571 | 867 | 13 | 5 | 38.4615 | |
| ckim-gatk | INDEL | I1_5 | map_l150_m2_e0 | homalt | 99.0099 | 99.5025 | 98.5222 | 88.8462 | 200 | 1 | 200 | 3 | 2 | 66.6667 | |
| gduggal-bwaplat | INDEL | I1_5 | map_l100_m0_e0 | het | 75.6144 | 61.3497 | 98.5222 | 94.8055 | 200 | 126 | 200 | 3 | 1 | 33.3333 | |
| gduggal-bwafb | INDEL | I1_5 | map_l150_m2_e0 | homalt | 99.0099 | 99.5025 | 98.5222 | 89.2706 | 200 | 1 | 200 | 3 | 1 | 33.3333 | |
| ndellapenna-hhga | INDEL | I1_5 | map_l150_m2_e0 | homalt | 99.0099 | 99.5025 | 98.5222 | 88.8031 | 200 | 1 | 200 | 3 | 1 | 33.3333 | |
| dgrover-gatk | INDEL | I1_5 | map_l150_m2_e0 | homalt | 99.0099 | 99.5025 | 98.5222 | 88.5634 | 200 | 1 | 200 | 3 | 2 | 66.6667 | |
| hfeng-pmm2 | SNP | * | map_l150_m0_e0 | * | 98.8358 | 99.1523 | 98.5214 | 81.5215 | 11930 | 102 | 11927 | 179 | 19 | 10.6145 | |
| rpoplin-dv42 | INDEL | I1_5 | map_l100_m0_e0 | * | 98.1543 | 97.7901 | 98.5213 | 84.3687 | 531 | 12 | 533 | 8 | 3 | 37.5000 | |
| gduggal-snapvard | INDEL | * | map_l150_m1_e0 | homalt | 92.4102 | 87.0130 | 98.5213 | 84.2778 | 402 | 60 | 533 | 8 | 6 | 75.0000 | |
| hfeng-pmm2 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 97.0630 | 95.6476 | 98.5210 | 73.1357 | 901 | 41 | 866 | 13 | 7 | 53.8462 | |
| jmaeng-gatk | SNP | ti | map_l100_m1_e0 | * | 89.7569 | 82.4247 | 98.5209 | 77.3729 | 39507 | 8424 | 39500 | 593 | 63 | 10.6239 | |
| rpoplin-dv42 | SNP | ti | map_l250_m2_e0 | het | 98.3531 | 98.1868 | 98.5199 | 88.5673 | 3195 | 59 | 3195 | 48 | 29 | 60.4167 | |
| mlin-fermikit | INDEL | I16_PLUS | * | hetalt | 66.4183 | 50.0953 | 98.5199 | 58.7247 | 1051 | 1047 | 1065 | 16 | 15 | 93.7500 | |
| mlin-fermikit | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 97.5756 | 96.6493 | 98.5199 | 55.4070 | 2596 | 90 | 2596 | 39 | 1 | 2.5641 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_51to200 | * | 96.0289 | 93.6620 | 98.5185 | 45.3441 | 133 | 9 | 133 | 2 | 2 | 100.0000 | |
| gduggal-snapvard | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 98.3899 | 98.2619 | 98.5182 | 61.1046 | 6897 | 122 | 6848 | 103 | 31 | 30.0971 | |
| rpoplin-dv42 | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 97.0809 | 95.6851 | 98.5179 | 60.2481 | 1264 | 57 | 1263 | 19 | 15 | 78.9474 | |
| dgrover-gatk | INDEL | D1_5 | map_l125_m2_e0 | * | 98.6027 | 98.6877 | 98.5179 | 88.1508 | 1128 | 15 | 1130 | 17 | 4 | 23.5294 | |
| bgallagher-sentieon | INDEL | D1_5 | map_l100_m2_e1 | * | 98.8190 | 99.1233 | 98.5166 | 84.7206 | 1922 | 17 | 1926 | 29 | 6 | 20.6897 | |
| dgrover-gatk | SNP | tv | map_l100_m0_e0 | het | 98.8895 | 99.2661 | 98.5157 | 76.1747 | 7169 | 53 | 7168 | 108 | 20 | 18.5185 | |
| ckim-dragen | INDEL | * | map_l100_m2_e1 | homalt | 98.5552 | 98.5948 | 98.5156 | 84.6468 | 1263 | 18 | 1261 | 19 | 10 | 52.6316 | |
| gduggal-snapvard | INDEL | * | map_l100_m2_e0 | homalt | 91.2669 | 85.0119 | 98.5155 | 76.6062 | 1072 | 189 | 1460 | 22 | 18 | 81.8182 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.9858 | 99.4610 | 98.5152 | 56.4669 | 6643 | 36 | 6635 | 100 | 98 | 98.0000 | |
| hfeng-pmm2 | SNP | tv | map_l125_m0_e0 | * | 98.7817 | 99.0499 | 98.5149 | 77.4668 | 6568 | 63 | 6567 | 99 | 13 | 13.1313 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.0050 | 99.5000 | 98.5149 | 62.6617 | 199 | 1 | 199 | 3 | 3 | 100.0000 | |
| jmaeng-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.0050 | 99.5000 | 98.5149 | 61.3027 | 199 | 1 | 199 | 3 | 3 | 100.0000 | |
| jmaeng-gatk | INDEL | I1_5 | map_l150_m2_e0 | homalt | 98.7593 | 99.0050 | 98.5149 | 88.5292 | 199 | 2 | 199 | 3 | 2 | 66.6667 | |
| mlin-fermikit | SNP | tv | segdup | * | 97.8523 | 97.1988 | 98.5147 | 87.3016 | 8293 | 239 | 8291 | 125 | 50 | 40.0000 | |
| gduggal-snapfb | SNP | ti | map_siren | * | 98.5881 | 98.6618 | 98.5145 | 58.3905 | 99012 | 1343 | 99014 | 1493 | 523 | 35.0301 | |