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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
26401-26450 / 86044 show all | |||||||||||||||
| ckim-isaac | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 87.1050 | 83.6066 | 90.9091 | 64.1694 | 102 | 20 | 100 | 10 | 2 | 20.0000 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.6856 | 99.9087 | 99.4636 | 76.0319 | 21879 | 20 | 21879 | 118 | 117 | 99.1525 | |
| ckim-vqsr | INDEL | I16_PLUS | HG002complexvar | hetalt | 96.6468 | 94.0299 | 99.4135 | 66.8932 | 315 | 20 | 339 | 2 | 2 | 100.0000 | |
| ckim-vqsr | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 93.9394 | 90.2913 | 97.8947 | 88.4988 | 186 | 20 | 186 | 4 | 2 | 50.0000 | |
| ckim-vqsr | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 97.8600 | 97.3046 | 98.4218 | 73.5584 | 722 | 20 | 686 | 11 | 5 | 45.4545 | |
| ckim-vqsr | SNP | * | HG002complexvar | hetalt | 96.6667 | 93.5484 | 100.0000 | 40.6953 | 290 | 20 | 290 | 0 | 0 | ||
| ckim-isaac | INDEL | I6_15 | map_l150_m2_e1 | * | 41.1765 | 25.9259 | 100.0000 | 97.8723 | 7 | 20 | 7 | 0 | 0 | ||
| ckim-vqsr | INDEL | * | map_l125_m0_e0 | het | 95.3743 | 96.5928 | 94.1860 | 94.0596 | 567 | 20 | 567 | 35 | 1 | 2.8571 | |
| ckim-vqsr | INDEL | * | segdup | het | 98.4343 | 98.6357 | 98.2337 | 96.7022 | 1446 | 20 | 1446 | 26 | 1 | 3.8462 | |
| ckim-vqsr | SNP | tv | HG002complexvar | hetalt | 96.6667 | 93.5484 | 100.0000 | 40.6953 | 290 | 20 | 290 | 0 | 0 | ||
| dgrover-gatk | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.4228 | 99.0946 | 92.0135 | 66.0676 | 2189 | 20 | 2189 | 190 | 184 | 96.8421 | |
| dgrover-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.5418 | 99.9350 | 99.1517 | 74.5652 | 30741 | 20 | 30741 | 263 | 257 | 97.7186 | |
| dgrover-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | hetalt | 93.6306 | 88.0240 | 100.0000 | 68.6848 | 147 | 20 | 150 | 0 | 0 | ||
| dgrover-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 98.1914 | 99.7899 | 96.6433 | 56.0900 | 9501 | 20 | 9501 | 330 | 327 | 99.0909 | |
| dgrover-gatk | INDEL | * | map_l100_m0_e0 | het | 97.5662 | 98.0411 | 97.0958 | 88.5957 | 1001 | 20 | 1003 | 30 | 4 | 13.3333 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | * | 96.9781 | 96.7532 | 97.2039 | 68.1675 | 596 | 20 | 591 | 17 | 15 | 88.2353 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 83.0580 | 85.1852 | 81.0345 | 77.8626 | 115 | 20 | 94 | 22 | 21 | 95.4545 | |
| ckim-vqsr | SNP | ti | map_l100_m2_e1 | hetalt | 55.8140 | 38.7097 | 100.0000 | 93.1034 | 12 | 19 | 12 | 0 | 0 | ||
| ckim-vqsr | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 99.1719 | 98.7467 | 99.6008 | 69.5995 | 1497 | 19 | 1497 | 6 | 2 | 33.3333 | |
| ckim-vqsr | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | * | 99.6806 | 99.6087 | 99.7525 | 66.7490 | 4837 | 19 | 4837 | 12 | 10 | 83.3333 | |
| dgrover-gatk | INDEL | * | map_l150_m2_e1 | het | 97.7901 | 97.9437 | 97.6369 | 91.8626 | 905 | 19 | 909 | 22 | 3 | 13.6364 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 96.4629 | 98.9555 | 94.0928 | 85.7865 | 1800 | 19 | 1561 | 98 | 66 | 67.3469 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 96.4629 | 98.9555 | 94.0928 | 85.7865 | 1800 | 19 | 1561 | 98 | 66 | 67.3469 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.8920 | 97.5066 | 98.2804 | 67.0301 | 743 | 19 | 743 | 13 | 7 | 53.8462 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.2738 | 99.4197 | 97.1540 | 68.7190 | 3255 | 19 | 3243 | 95 | 92 | 96.8421 | |
| egarrison-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.6133 | 99.5263 | 99.7004 | 48.1016 | 3992 | 19 | 3993 | 12 | 3 | 25.0000 | |
| egarrison-hhga | SNP | ti | map_l125_m0_e0 | homalt | 99.7435 | 99.5769 | 99.9106 | 67.7962 | 4472 | 19 | 4472 | 4 | 4 | 100.0000 | |
| egarrison-hhga | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 97.5081 | 95.9488 | 99.1189 | 81.2706 | 450 | 19 | 450 | 4 | 2 | 50.0000 | |
| eyeh-varpipe | INDEL | * | map_l100_m0_e0 | hetalt | 58.2726 | 42.4242 | 93.0233 | 93.1746 | 14 | 19 | 40 | 3 | 2 | 66.6667 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 98.9371 | 98.3926 | 99.4876 | 28.3354 | 1163 | 19 | 1165 | 6 | 6 | 100.0000 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 93.9523 | 95.2381 | 92.7007 | 57.3209 | 380 | 19 | 381 | 30 | 18 | 60.0000 | |
| egarrison-hhga | INDEL | D16_PLUS | map_siren | hetalt | 54.6410 | 38.7097 | 92.8571 | 81.8182 | 12 | 19 | 13 | 1 | 0 | 0.0000 | |
| egarrison-hhga | INDEL | D1_5 | map_l125_m2_e1 | * | 98.3578 | 98.3578 | 98.3578 | 86.6797 | 1138 | 19 | 1138 | 19 | 6 | 31.5789 | |
| egarrison-hhga | INDEL | I16_PLUS | HG002complexvar | homalt | 93.4091 | 93.8511 | 92.9712 | 64.6727 | 290 | 19 | 291 | 22 | 18 | 81.8182 | |
| egarrison-hhga | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 84.3305 | 80.0000 | 89.1566 | 86.2583 | 76 | 19 | 74 | 9 | 4 | 44.4444 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 93.7833 | 93.2862 | 94.2857 | 69.6641 | 264 | 19 | 264 | 16 | 13 | 81.2500 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 98.6821 | 98.0105 | 99.3631 | 78.4932 | 936 | 19 | 936 | 6 | 3 | 50.0000 | |
| ckim-isaac | INDEL | I6_15 | map_l150_m1_e0 | * | 38.7097 | 24.0000 | 100.0000 | 97.4265 | 6 | 19 | 7 | 0 | 0 | ||
| ckim-isaac | INDEL | I6_15 | map_l150_m2_e0 | * | 38.7097 | 24.0000 | 100.0000 | 97.7848 | 6 | 19 | 7 | 0 | 0 | ||
| ckim-isaac | SNP | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 65.7143 | 54.7619 | 82.1429 | 95.6923 | 23 | 19 | 23 | 5 | 0 | 0.0000 | |
| ckim-isaac | SNP | * | tech_badpromoters | * | 93.2432 | 87.8981 | 99.2806 | 31.5271 | 138 | 19 | 138 | 1 | 0 | 0.0000 | |
| ckim-vqsr | INDEL | * | map_siren | homalt | 99.3599 | 99.2844 | 99.4355 | 81.7137 | 2636 | 19 | 2642 | 15 | 8 | 53.3333 | |
| ckim-isaac | INDEL | D16_PLUS | map_l125_m1_e0 | het | 9.0909 | 5.0000 | 50.0000 | 98.4375 | 1 | 19 | 1 | 1 | 0 | 0.0000 | |
| ckim-isaac | INDEL | D16_PLUS | map_l125_m2_e0 | het | 9.0909 | 5.0000 | 50.0000 | 98.6014 | 1 | 19 | 1 | 1 | 0 | 0.0000 | |
| ckim-isaac | INDEL | D16_PLUS | map_l125_m2_e1 | het | 9.0909 | 5.0000 | 50.0000 | 98.6207 | 1 | 19 | 1 | 1 | 0 | 0.0000 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | hetalt | 81.5419 | 72.4638 | 93.2203 | 60.1351 | 50 | 19 | 55 | 4 | 4 | 100.0000 | |
| ckim-isaac | INDEL | D6_15 | map_l125_m2_e0 | homalt | 64.1509 | 47.2222 | 100.0000 | 75.7143 | 17 | 19 | 17 | 0 | 0 | ||
| ckim-isaac | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 56.9192 | 62.7451 | 52.0833 | 91.3514 | 32 | 19 | 25 | 23 | 2 | 8.6957 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 96.0637 | 95.9574 | 96.1702 | 60.0680 | 451 | 19 | 452 | 18 | 6 | 33.3333 | |
| ckim-isaac | INDEL | I6_15 | HG002compoundhet | homalt | 15.7021 | 38.7097 | 9.8485 | 69.8630 | 12 | 19 | 13 | 119 | 118 | 99.1597 | |