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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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
24501-24550 / 86044 show all | |||||||||||||||
| dgrover-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.3899 | 99.7736 | 97.0441 | 62.0464 | 11458 | 26 | 11458 | 349 | 339 | 97.1347 | |
| dgrover-gatk | INDEL | * | map_l125_m1_e0 | het | 97.9822 | 98.0524 | 97.9120 | 89.0949 | 1309 | 26 | 1313 | 28 | 4 | 14.2857 | |
| ckim-vqsr | INDEL | D1_5 | map_l100_m0_e0 | * | 96.7071 | 96.9873 | 96.4286 | 89.7798 | 837 | 26 | 837 | 31 | 4 | 12.9032 | |
| ckim-vqsr | INDEL | D1_5 | map_l150_m2_e1 | het | 94.6619 | 95.0192 | 94.3074 | 93.7699 | 496 | 26 | 497 | 30 | 3 | 10.0000 | |
| ckim-vqsr | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.5047 | 99.0504 | 99.9631 | 30.7908 | 2712 | 26 | 2712 | 1 | 1 | 100.0000 | |
| ckim-vqsr | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 98.9599 | 98.7154 | 99.2056 | 68.9820 | 1998 | 26 | 1998 | 16 | 7 | 43.7500 | |
| ckim-vqsr | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 99.3564 | 99.1213 | 99.5925 | 49.2504 | 2933 | 26 | 2933 | 12 | 3 | 25.0000 | |
| ckim-vqsr | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 99.4334 | 99.3865 | 99.4804 | 79.7057 | 4212 | 26 | 4212 | 22 | 8 | 36.3636 | |
| ckim-vqsr | SNP | ti | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.3604 | 98.8187 | 99.9081 | 42.3617 | 2175 | 26 | 2175 | 2 | 2 | 100.0000 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | het | 56.2300 | 84.6154 | 42.1053 | 63.3609 | 143 | 26 | 56 | 77 | 75 | 97.4026 | |
| ckim-isaac | INDEL | D6_15 | map_l100_m2_e1 | hetalt | 77.6993 | 64.3836 | 97.9592 | 68.5897 | 47 | 26 | 48 | 1 | 1 | 100.0000 | |
| ckim-isaac | INDEL | I16_PLUS | map_l100_m1_e0 | * | 0.0000 | 100.0000 | 0 | 26 | 0 | 0 | 0 | ||||
| ckim-isaac | INDEL | I16_PLUS | map_l100_m2_e0 | * | 0.0000 | 100.0000 | 0 | 26 | 0 | 0 | 0 | ||||
| ckim-isaac | INDEL | I16_PLUS | map_l100_m2_e1 | * | 0.0000 | 100.0000 | 0 | 26 | 0 | 0 | 0 | ||||
| ckim-isaac | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 94.8810 | 91.7722 | 98.2079 | 71.1479 | 290 | 26 | 274 | 5 | 4 | 80.0000 | |
| ckim-isaac | INDEL | I1_5 | map_siren | hetalt | 85.4934 | 76.7857 | 96.4286 | 82.2410 | 86 | 26 | 81 | 3 | 2 | 66.6667 | |
| dgrover-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 95.7596 | 92.3754 | 99.4012 | 59.5152 | 315 | 26 | 332 | 2 | 2 | 100.0000 | |
| dgrover-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 98.8372 | 97.7011 | 100.0000 | 42.5246 | 1105 | 26 | 1111 | 0 | 0 | ||
| dgrover-gatk | INDEL | I1_5 | map_siren | * | 99.2843 | 99.1348 | 99.4343 | 81.3909 | 2979 | 26 | 2988 | 17 | 5 | 29.4118 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 82.5000 | 71.7391 | 97.0588 | 60.2339 | 66 | 26 | 66 | 2 | 1 | 50.0000 | |
| dgrover-gatk | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 99.7832 | 99.7317 | 99.8347 | 68.1691 | 9666 | 26 | 9666 | 16 | 12 | 75.0000 | |
| egarrison-hhga | INDEL | * | map_l125_m0_e0 | * | 97.3294 | 97.0522 | 97.6082 | 98.7845 | 856 | 26 | 857 | 21 | 7 | 33.3333 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 81.7599 | 69.8795 | 98.5075 | 30.9278 | 58 | 25 | 66 | 1 | 1 | 100.0000 | |
| dgrover-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 99.2355 | 99.0692 | 99.4023 | 51.3626 | 2661 | 25 | 2661 | 16 | 1 | 6.2500 | |
| dgrover-gatk | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.6673 | 99.8600 | 99.4754 | 57.8446 | 17826 | 25 | 17825 | 94 | 5 | 5.3192 | |
| egarrison-hhga | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | het | 80.0000 | 71.2644 | 91.1765 | 99.9005 | 62 | 25 | 62 | 6 | 2 | 33.3333 | |
| dgrover-gatk | INDEL | D1_5 | * | homalt | 99.8204 | 99.9489 | 99.6922 | 62.5668 | 48901 | 25 | 48906 | 151 | 149 | 98.6755 | |
| dgrover-gatk | INDEL | D1_5 | map_siren | * | 99.2924 | 99.2916 | 99.2932 | 82.3565 | 3504 | 25 | 3512 | 25 | 5 | 20.0000 | |
| ckim-isaac | INDEL | I6_15 | map_l100_m1_e0 | homalt | 39.0244 | 24.2424 | 100.0000 | 90.0000 | 8 | 25 | 8 | 0 | 0 | ||
| ckim-isaac | INDEL | I6_15 | map_l100_m2_e0 | homalt | 39.0244 | 24.2424 | 100.0000 | 90.8046 | 8 | 25 | 8 | 0 | 0 | ||
| ckim-isaac | INDEL | I6_15 | map_l100_m2_e1 | homalt | 39.0244 | 24.2424 | 100.0000 | 90.9091 | 8 | 25 | 8 | 0 | 0 | ||
| ckim-isaac | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 84.6065 | 77.2727 | 93.4783 | 86.4507 | 85 | 25 | 86 | 6 | 4 | 66.6667 | |
| ckim-vqsr | INDEL | D16_PLUS | HG002complexvar | hetalt | 93.2896 | 89.8785 | 96.9697 | 47.4403 | 222 | 25 | 448 | 14 | 14 | 100.0000 | |
| egarrison-hhga | SNP | tv | map_l100_m1_e0 | homalt | 99.8284 | 99.7235 | 99.9335 | 62.1365 | 9018 | 25 | 9018 | 6 | 5 | 83.3333 | |
| egarrison-hhga | SNP | tv | map_l100_m2_e0 | homalt | 99.8316 | 99.7287 | 99.9347 | 64.6441 | 9189 | 25 | 9189 | 6 | 5 | 83.3333 | |
| egarrison-hhga | SNP | tv | map_l100_m2_e1 | homalt | 99.8332 | 99.7312 | 99.9354 | 64.6456 | 9277 | 25 | 9277 | 6 | 5 | 83.3333 | |
| eyeh-varpipe | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | het | 59.5745 | 50.0000 | 73.6842 | 74.3243 | 25 | 25 | 28 | 10 | 7 | 70.0000 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 91.8769 | 85.4651 | 99.3289 | 73.0072 | 147 | 25 | 148 | 1 | 0 | 0.0000 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_gt10 | het | 51.8908 | 43.1818 | 65.0000 | 89.0710 | 19 | 25 | 13 | 7 | 3 | 42.8571 | |
| ckim-isaac | INDEL | D16_PLUS | map_l125_m2_e1 | * | 18.7500 | 10.7143 | 75.0000 | 97.8610 | 3 | 25 | 3 | 1 | 0 | 0.0000 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | het | 53.2627 | 83.1081 | 39.1892 | 51.8438 | 123 | 25 | 87 | 135 | 134 | 99.2593 | |
| ckim-isaac | INDEL | I1_5 | segdup | homalt | 97.0748 | 94.7146 | 99.5556 | 90.3516 | 448 | 25 | 448 | 2 | 2 | 100.0000 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 95.9006 | 93.9173 | 97.9695 | 71.5112 | 386 | 25 | 386 | 8 | 8 | 100.0000 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 77.9560 | 93.5065 | 66.8403 | 62.4021 | 360 | 25 | 385 | 191 | 169 | 88.4817 | |
| egarrison-hhga | INDEL | D1_5 | segdup | * | 97.7335 | 97.7335 | 97.7335 | 94.3200 | 1078 | 25 | 1078 | 25 | 22 | 88.0000 | |
| egarrison-hhga | INDEL | D6_15 | HG002complexvar | homalt | 95.9329 | 97.8614 | 94.0789 | 59.2766 | 1144 | 25 | 1144 | 72 | 43 | 59.7222 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 89.7762 | 88.0383 | 91.5842 | 74.4949 | 184 | 25 | 185 | 17 | 10 | 58.8235 | |
| egarrison-hhga | INDEL | D6_15 | segdup | * | 91.4691 | 86.9110 | 96.5318 | 93.2842 | 166 | 25 | 167 | 6 | 6 | 100.0000 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 98.6785 | 97.8849 | 99.4850 | 27.6398 | 1157 | 25 | 1159 | 6 | 6 | 100.0000 | |
| ckim-vqsr | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 94.9718 | 91.0394 | 99.2593 | 62.7586 | 254 | 25 | 268 | 2 | 2 | 100.0000 | |