PrecisionFDA
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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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
46651-46700 / 86044 show all | |||||||||||||||
| jlack-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | * | 98.7179 | 98.0892 | 99.3548 | 69.6078 | 154 | 3 | 154 | 1 | 0 | 0.0000 | |
| jlack-gatk | INDEL | D16_PLUS | map_l100_m0_e0 | het | 77.2947 | 84.2105 | 71.4286 | 97.1429 | 16 | 3 | 15 | 6 | 0 | 0.0000 | |
| jlack-gatk | INDEL | D16_PLUS | map_l125_m2_e1 | * | 86.2069 | 89.2857 | 83.3333 | 97.4116 | 25 | 3 | 25 | 5 | 1 | 20.0000 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.8372 | 98.8372 | 98.8372 | 62.4454 | 255 | 3 | 255 | 3 | 2 | 66.6667 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | hetalt | 94.4444 | 91.8919 | 97.1429 | 87.8472 | 34 | 3 | 34 | 1 | 1 | 100.0000 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.8365 | 99.9182 | 99.7549 | 50.2169 | 3663 | 3 | 3663 | 9 | 9 | 100.0000 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 99.5662 | 99.3506 | 99.7826 | 28.3489 | 459 | 3 | 459 | 1 | 1 | 100.0000 | |
| jlack-gatk | INDEL | D1_5 | map_l125_m0_e0 | homalt | 98.6395 | 97.9730 | 99.3151 | 86.1611 | 145 | 3 | 145 | 1 | 1 | 100.0000 | |
| jlack-gatk | INDEL | D1_5 | map_l250_m1_e0 | * | 89.6000 | 98.2456 | 82.3529 | 96.3309 | 168 | 3 | 168 | 36 | 1 | 2.7778 | |
| jlack-gatk | INDEL | D1_5 | map_l250_m2_e0 | * | 90.2743 | 98.3696 | 83.4101 | 96.5457 | 181 | 3 | 181 | 36 | 1 | 2.7778 | |
| jlack-gatk | INDEL | D1_5 | map_l250_m2_e1 | * | 90.3226 | 98.3784 | 83.4862 | 96.6186 | 182 | 3 | 182 | 36 | 1 | 2.7778 | |
| jlack-gatk | INDEL | D1_5 | segdup | hetalt | 97.0297 | 94.2308 | 100.0000 | 95.7018 | 49 | 3 | 49 | 0 | 0 | ||
| jlack-gatk | INDEL | D6_15 | HG002complexvar | homalt | 99.0234 | 99.7434 | 98.3137 | 61.3807 | 1166 | 3 | 1166 | 20 | 19 | 95.0000 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.5374 | 99.6524 | 99.4226 | 63.8866 | 860 | 3 | 861 | 5 | 2 | 40.0000 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | hetalt | 93.7973 | 90.9091 | 96.8750 | 63.2184 | 30 | 3 | 31 | 1 | 1 | 100.0000 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 97.2274 | 98.8722 | 95.6364 | 82.7370 | 263 | 3 | 263 | 12 | 2 | 16.6667 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 94.4444 | 91.8919 | 97.1429 | 63.9175 | 34 | 3 | 34 | 1 | 1 | 100.0000 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_gt10 | hetalt | 60.0000 | 66.6667 | 54.5455 | 98.9413 | 6 | 3 | 6 | 5 | 0 | 0.0000 | |
| jlack-gatk | INDEL | D6_15 | map_l100_m0_e0 | hetalt | 88.8889 | 84.2105 | 94.1176 | 82.2917 | 16 | 3 | 16 | 1 | 0 | 0.0000 | |
| jlack-gatk | INDEL | D6_15 | map_l125_m1_e0 | het | 89.7059 | 95.3125 | 84.7222 | 93.7984 | 61 | 3 | 61 | 11 | 1 | 9.0909 | |
| jlack-gatk | INDEL | D6_15 | map_l125_m2_e1 | hetalt | 89.4737 | 85.0000 | 94.4444 | 86.3636 | 17 | 3 | 17 | 1 | 0 | 0.0000 | |
| jlack-gatk | INDEL | D6_15 | map_l150_m2_e1 | * | 93.1818 | 96.4706 | 90.1099 | 93.5825 | 82 | 3 | 82 | 9 | 1 | 11.1111 | |
| jlack-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 96.1351 | 95.4545 | 96.8254 | 89.0815 | 63 | 3 | 61 | 2 | 0 | 0.0000 | |
| jlack-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 98.1219 | 97.2222 | 99.0385 | 80.7050 | 105 | 3 | 103 | 1 | 0 | 0.0000 | |
| jlack-gatk | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | * | 33.3333 | 25.0000 | 50.0000 | 92.5926 | 1 | 3 | 1 | 1 | 0 | 0.0000 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.5000 | 98.5000 | 98.5000 | 60.9375 | 197 | 3 | 197 | 3 | 3 | 100.0000 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.2570 | 99.3617 | 99.1525 | 68.8860 | 467 | 3 | 468 | 4 | 3 | 75.0000 | |
| jlack-gatk | INDEL | I1_5 | map_l100_m1_e0 | homalt | 99.2293 | 99.4208 | 99.0385 | 80.7763 | 515 | 3 | 515 | 5 | 3 | 60.0000 | |
| jlack-gatk | INDEL | I1_5 | map_l125_m2_e0 | homalt | 98.9751 | 99.1202 | 98.8304 | 84.6843 | 338 | 3 | 338 | 4 | 2 | 50.0000 | |
| jlack-gatk | INDEL | I1_5 | map_l125_m2_e1 | homalt | 98.9811 | 99.1254 | 98.8372 | 84.8791 | 340 | 3 | 340 | 4 | 2 | 50.0000 | |
| jlack-gatk | INDEL | I1_5 | segdup | homalt | 99.4709 | 99.3658 | 99.5763 | 92.8690 | 470 | 3 | 470 | 2 | 2 | 100.0000 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 95.5882 | 99.5406 | 91.9378 | 72.4044 | 650 | 3 | 650 | 57 | 55 | 96.4912 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.0228 | 98.0645 | 100.0000 | 83.4056 | 152 | 3 | 153 | 0 | 0 | ||
| jlack-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 97.7064 | 98.6111 | 96.8182 | 66.6667 | 213 | 3 | 213 | 7 | 6 | 85.7143 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 95.5224 | 91.4286 | 100.0000 | 91.0394 | 32 | 3 | 25 | 0 | 0 | ||
| jlack-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.4012 | 99.2823 | 99.5204 | 47.6788 | 415 | 3 | 415 | 2 | 1 | 50.0000 | |
| jlack-gatk | INDEL | I6_15 | map_l100_m0_e0 | het | 80.0000 | 82.3529 | 77.7778 | 94.5619 | 14 | 3 | 14 | 4 | 0 | 0.0000 | |
| jlack-gatk | INDEL | I6_15 | map_l125_m0_e0 | * | 82.7586 | 80.0000 | 85.7143 | 96.2466 | 12 | 3 | 12 | 2 | 0 | 0.0000 | |
| jlack-gatk | INDEL | I6_15 | map_l125_m0_e0 | het | 70.5882 | 66.6667 | 75.0000 | 96.9582 | 6 | 3 | 6 | 2 | 0 | 0.0000 | |
| jlack-gatk | INDEL | I6_15 | map_l150_m1_e0 | * | 86.2745 | 88.0000 | 84.6154 | 95.7861 | 22 | 3 | 22 | 4 | 0 | 0.0000 | |
| jlack-gatk | INDEL | I6_15 | map_l150_m1_e0 | het | 80.0000 | 80.0000 | 80.0000 | 96.4539 | 12 | 3 | 12 | 3 | 0 | 0.0000 | |
| jlack-gatk | INDEL | I6_15 | map_l150_m2_e0 | * | 86.2745 | 88.0000 | 84.6154 | 96.2963 | 22 | 3 | 22 | 4 | 0 | 0.0000 | |
| jlack-gatk | INDEL | I6_15 | map_l150_m2_e0 | het | 80.0000 | 80.0000 | 80.0000 | 96.8553 | 12 | 3 | 12 | 3 | 0 | 0.0000 | |
| jlack-gatk | INDEL | I6_15 | map_l150_m2_e1 | * | 87.2727 | 88.8889 | 85.7143 | 96.1433 | 24 | 3 | 24 | 4 | 0 | 0.0000 | |
| jlack-gatk | INDEL | I6_15 | map_l150_m2_e1 | het | 81.2500 | 81.2500 | 81.2500 | 96.7546 | 13 | 3 | 13 | 3 | 0 | 0.0000 | |
| jlack-gatk | INDEL | I6_15 | segdup | hetalt | 96.5517 | 93.3333 | 100.0000 | 90.3448 | 42 | 3 | 42 | 0 | 0 | ||
| jlack-gatk | SNP | * | HG002complexvar | hetalt | 99.0323 | 99.0323 | 99.0323 | 39.5712 | 307 | 3 | 307 | 3 | 3 | 100.0000 | |
| jlack-gatk | SNP | * | func_cds | het | 98.8875 | 99.9731 | 97.8251 | 36.6500 | 11158 | 3 | 11155 | 248 | 1 | 0.4032 | |
| jlack-gatk | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.9343 | 99.9507 | 99.9179 | 54.3410 | 6085 | 3 | 6085 | 5 | 5 | 100.0000 | |
| jlack-gatk | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.9087 | 99.8904 | 99.9269 | 30.4624 | 2735 | 3 | 2735 | 2 | 2 | 100.0000 | |