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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
56301-56350 / 86044 show all | |||||||||||||||
| ckim-isaac | SNP | ti | map_l125_m2_e0 | hetalt | 66.6667 | 50.0000 | 100.0000 | 78.1818 | 12 | 12 | 12 | 0 | 0 | ||
| ckim-isaac | SNP | ti | map_l125_m2_e1 | hetalt | 66.6667 | 50.0000 | 100.0000 | 78.1818 | 12 | 12 | 12 | 0 | 0 | ||
| ckim-isaac | SNP | tv | map_l150_m1_e0 | hetalt | 57.1429 | 40.0000 | 100.0000 | 85.7143 | 8 | 12 | 8 | 0 | 0 | ||
| ckim-isaac | SNP | tv | map_l150_m2_e0 | hetalt | 57.1429 | 40.0000 | 100.0000 | 87.0968 | 8 | 12 | 8 | 0 | 0 | ||
| ckim-isaac | SNP | tv | map_l150_m2_e1 | hetalt | 57.1429 | 40.0000 | 100.0000 | 87.3016 | 8 | 12 | 8 | 0 | 0 | ||
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 93.5626 | 98.9848 | 88.7036 | 60.4379 | 1170 | 12 | 1170 | 149 | 147 | 98.6577 | |
| ckim-vqsr | INDEL | * | map_l150_m0_e0 | het | 93.8659 | 96.4809 | 91.3889 | 95.6752 | 329 | 12 | 329 | 31 | 0 | 0.0000 | |
| ckim-vqsr | INDEL | * | map_l250_m1_e0 | het | 90.3553 | 93.6842 | 87.2549 | 97.7493 | 178 | 12 | 178 | 26 | 1 | 3.8462 | |
| ckim-vqsr | INDEL | D1_5 | map_l125_m0_e0 | * | 96.4143 | 97.5806 | 95.2756 | 92.2773 | 484 | 12 | 484 | 24 | 3 | 12.5000 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.5654 | 99.3064 | 99.8258 | 36.8073 | 1718 | 12 | 1719 | 3 | 3 | 100.0000 | |
| ckim-vqsr | INDEL | D6_15 | map_l100_m2_e0 | * | 96.0000 | 95.4545 | 96.5517 | 89.8325 | 252 | 12 | 252 | 9 | 2 | 22.2222 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.4113 | 99.1196 | 99.7048 | 77.3525 | 1351 | 12 | 1351 | 4 | 2 | 50.0000 | |
| ckim-vqsr | INDEL | I1_5 | segdup | * | 99.0079 | 98.8669 | 99.1493 | 95.7156 | 1047 | 12 | 1049 | 9 | 2 | 22.2222 | |
| ckim-vqsr | INDEL | I6_15 | map_siren | * | 97.5042 | 96.0656 | 98.9865 | 86.0902 | 293 | 12 | 293 | 3 | 1 | 33.3333 | |
| ckim-vqsr | SNP | * | lowcmp_SimpleRepeat_quadTR_51to200 | * | 94.2446 | 91.6084 | 97.0370 | 92.7807 | 131 | 12 | 131 | 4 | 3 | 75.0000 | |
| ckim-vqsr | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | het | 99.7614 | 99.6188 | 99.9044 | 71.9607 | 3136 | 12 | 3136 | 3 | 3 | 100.0000 | |
| ckim-vqsr | SNP | ti | map_l100_m0_e0 | hetalt | 25.0000 | 14.2857 | 100.0000 | 97.2973 | 2 | 12 | 2 | 0 | 0 | ||
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 52.4345 | 36.8421 | 90.9091 | 71.0526 | 7 | 12 | 10 | 1 | 1 | 100.0000 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 98.4653 | 97.5659 | 99.3814 | 54.5880 | 481 | 12 | 482 | 3 | 3 | 100.0000 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.7987 | 99.8821 | 99.7155 | 54.3488 | 10166 | 12 | 10164 | 29 | 24 | 82.7586 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 96.1039 | 93.9086 | 98.4043 | 52.4051 | 185 | 12 | 185 | 3 | 3 | 100.0000 | |
| egarrison-hhga | INDEL | D1_5 | map_l150_m1_e0 | het | 97.5104 | 97.5104 | 97.5104 | 88.0782 | 470 | 12 | 470 | 12 | 2 | 16.6667 | |
| egarrison-hhga | INDEL | D1_5 | map_l150_m2_e0 | het | 97.6654 | 97.6654 | 97.6654 | 88.5803 | 502 | 12 | 502 | 12 | 2 | 16.6667 | |
| egarrison-hhga | INDEL | D1_5 | map_l150_m2_e1 | het | 97.7011 | 97.7011 | 97.7011 | 88.5827 | 510 | 12 | 510 | 12 | 2 | 16.6667 | |
| egarrison-hhga | INDEL | D6_15 | map_l125_m2_e1 | * | 92.4953 | 90.6250 | 94.4444 | 89.0720 | 116 | 12 | 119 | 7 | 5 | 71.4286 | |
| egarrison-hhga | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | * | 66.4234 | 53.8462 | 86.6667 | 90.1316 | 14 | 12 | 13 | 2 | 1 | 50.0000 | |
| egarrison-hhga | INDEL | I1_5 | map_l100_m1_e0 | het | 98.5825 | 98.4556 | 98.7097 | 83.9478 | 765 | 12 | 765 | 10 | 1 | 10.0000 | |
| egarrison-hhga | INDEL | I1_5 | map_l100_m2_e0 | het | 98.5489 | 98.4868 | 98.6111 | 85.1044 | 781 | 12 | 781 | 11 | 1 | 9.0909 | |
| egarrison-hhga | INDEL | I1_5 | map_l125_m2_e0 | * | 98.7150 | 98.5998 | 98.8304 | 87.2578 | 845 | 12 | 845 | 10 | 2 | 20.0000 | |
| egarrison-hhga | INDEL | I1_5 | map_l125_m2_e1 | * | 98.7342 | 98.6207 | 98.8479 | 87.4221 | 858 | 12 | 858 | 10 | 2 | 20.0000 | |
| egarrison-hhga | INDEL | I1_5 | segdup | het | 98.2247 | 97.7695 | 98.6842 | 94.9835 | 526 | 12 | 525 | 7 | 1 | 14.2857 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 91.6667 | 93.6170 | 89.7959 | 66.0312 | 176 | 12 | 176 | 20 | 17 | 85.0000 | |
| egarrison-hhga | INDEL | I6_15 | map_siren | het | 95.2727 | 91.6084 | 99.2424 | 83.0769 | 131 | 12 | 131 | 1 | 1 | 100.0000 | |
| egarrison-hhga | SNP | ti | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.8153 | 99.7048 | 99.9260 | 44.7261 | 4053 | 12 | 4053 | 3 | 2 | 66.6667 | |
| egarrison-hhga | SNP | ti | map_l150_m0_e0 | homalt | 99.7098 | 99.5654 | 99.8547 | 73.4497 | 2749 | 12 | 2749 | 4 | 4 | 100.0000 | |
| eyeh-varpipe | INDEL | * | map_l250_m1_e0 | * | 96.2226 | 96.0656 | 96.3801 | 98.1181 | 293 | 12 | 426 | 16 | 10 | 62.5000 | |
| dgrover-gatk | INDEL | D6_15 | map_l100_m2_e0 | * | 96.1832 | 95.4545 | 96.9231 | 88.0624 | 252 | 12 | 252 | 8 | 2 | 25.0000 | |
| dgrover-gatk | INDEL | I16_PLUS | HG002complexvar | hetalt | 97.8993 | 96.4179 | 99.4269 | 69.1424 | 323 | 12 | 347 | 2 | 2 | 100.0000 | |
| dgrover-gatk | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 95.8025 | 94.1748 | 97.4874 | 88.3830 | 194 | 12 | 194 | 5 | 2 | 40.0000 | |
| dgrover-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 96.6277 | 95.1220 | 98.1818 | 88.6246 | 234 | 12 | 216 | 4 | 2 | 50.0000 | |
| dgrover-gatk | INDEL | I1_5 | HG002compoundhet | het | 95.2481 | 98.5882 | 92.1269 | 86.8653 | 838 | 12 | 784 | 67 | 66 | 98.5075 | |
| dgrover-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 99.3716 | 99.1196 | 99.6249 | 78.0612 | 1351 | 12 | 1328 | 5 | 3 | 60.0000 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.3958 | 98.0100 | 98.7847 | 73.2093 | 591 | 12 | 569 | 7 | 3 | 42.8571 | |
| dgrover-gatk | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.8260 | 99.6527 | 100.0000 | 62.8065 | 3443 | 12 | 3443 | 0 | 0 | ||
| dgrover-gatk | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 99.0399 | 98.7903 | 99.2908 | 71.3498 | 980 | 12 | 980 | 7 | 2 | 28.5714 | |
| dgrover-gatk | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.9175 | 99.8900 | 99.9450 | 60.3037 | 10899 | 12 | 10895 | 6 | 5 | 83.3333 | |
| dgrover-gatk | SNP | tv | segdup | het | 99.5280 | 99.7730 | 99.2842 | 92.5335 | 5275 | 12 | 5271 | 38 | 0 | 0.0000 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 90.9744 | 92.2581 | 89.7260 | 80.4813 | 143 | 12 | 131 | 15 | 3 | 20.0000 | |
| ckim-isaac | INDEL | D6_15 | map_l250_m1_e0 | * | 48.0000 | 33.3333 | 85.7143 | 97.3485 | 6 | 12 | 6 | 1 | 1 | 100.0000 | |
| ckim-isaac | INDEL | D6_15 | segdup | het | 89.7285 | 86.9565 | 92.6829 | 92.5319 | 80 | 12 | 76 | 6 | 6 | 100.0000 | |