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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
25051-25100 / 86044 show all | |||||||||||||||
| ckim-dragen | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.7926 | 99.8634 | 99.7220 | 66.5121 | 17544 | 24 | 17576 | 49 | 13 | 26.5306 | |
| ckim-gatk | INDEL | * | map_l150_m2_e1 | * | 95.7468 | 98.3322 | 93.2939 | 93.1304 | 1415 | 24 | 1419 | 102 | 10 | 9.8039 | |
| ckim-gatk | INDEL | D1_5 | map_l100_m2_e0 | * | 97.0041 | 98.7467 | 95.3219 | 88.2074 | 1891 | 24 | 1895 | 93 | 8 | 8.6022 | |
| ckim-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 95.2891 | 91.6084 | 99.2780 | 52.0761 | 262 | 24 | 275 | 2 | 2 | 100.0000 | |
| ckim-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.0984 | 99.3619 | 98.8363 | 71.4448 | 3737 | 24 | 3737 | 44 | 44 | 100.0000 | |
| ckim-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.0984 | 99.3619 | 98.8363 | 71.4448 | 3737 | 24 | 3737 | 44 | 44 | 100.0000 | |
| ckim-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 83.9506 | 73.9130 | 97.1429 | 57.8313 | 68 | 24 | 68 | 2 | 1 | 50.0000 | |
| ckim-gatk | SNP | * | func_cds | * | 99.6618 | 99.8678 | 99.4567 | 31.5863 | 18126 | 24 | 18123 | 99 | 1 | 1.0101 | |
| ckim-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 99.2628 | 99.1167 | 99.4094 | 87.9803 | 2693 | 24 | 2693 | 16 | 14 | 87.5000 | |
| ckim-gatk | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.6646 | 99.3826 | 99.9483 | 59.5457 | 3863 | 24 | 3863 | 2 | 2 | 100.0000 | |
| ckim-gatk | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.8353 | 99.6779 | 98.0069 | 41.1938 | 7428 | 24 | 7425 | 151 | 1 | 0.6623 | |
| ckim-dragen | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 99.0896 | 98.3925 | 99.7967 | 32.3556 | 1469 | 24 | 1473 | 3 | 3 | 100.0000 | |
| ckim-dragen | INDEL | D1_5 | map_l100_m1_e0 | het | 96.9291 | 98.0149 | 95.8671 | 85.7209 | 1185 | 24 | 1183 | 51 | 4 | 7.8431 | |
| ckim-dragen | INDEL | D1_5 | map_l100_m2_e0 | het | 97.0429 | 98.0892 | 96.0187 | 86.4645 | 1232 | 24 | 1230 | 51 | 4 | 7.8431 | |
| ckim-dragen | INDEL | D1_5 | map_l100_m2_e1 | het | 97.0706 | 98.1073 | 96.0557 | 86.5634 | 1244 | 24 | 1242 | 51 | 4 | 7.8431 | |
| ckim-dragen | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.5033 | 96.1905 | 98.8525 | 65.9408 | 606 | 24 | 603 | 7 | 6 | 85.7143 | |
| ckim-dragen | INDEL | I1_5 | map_l150_m2_e1 | het | 93.6184 | 92.4290 | 94.8387 | 92.0082 | 293 | 24 | 294 | 16 | 2 | 12.5000 | |
| ckim-dragen | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.7859 | 99.8680 | 99.7039 | 39.7224 | 18159 | 24 | 18186 | 54 | 6 | 11.1111 | |
| cchapple-custom | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.5931 | 99.3054 | 99.8825 | 45.7630 | 3431 | 24 | 3401 | 4 | 4 | 100.0000 | |
| cchapple-custom | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 98.1287 | 97.5806 | 98.6829 | 71.9841 | 968 | 24 | 974 | 13 | 0 | 0.0000 | |
| cchapple-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.7596 | 99.5574 | 99.9627 | 68.6053 | 5399 | 24 | 5353 | 2 | 2 | 100.0000 | |
| cchapple-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.7596 | 99.5574 | 99.9627 | 68.6053 | 5399 | 24 | 5353 | 2 | 2 | 100.0000 | |
| ciseli-custom | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | het | 73.3791 | 60.6557 | 92.8571 | 56.2500 | 37 | 24 | 39 | 3 | 3 | 100.0000 | |
| ciseli-custom | INDEL | D6_15 | map_l150_m2_e0 | het | 50.0000 | 47.8261 | 52.3810 | 95.3998 | 22 | 24 | 22 | 20 | 4 | 20.0000 | |
| ciseli-custom | INDEL | D6_15 | map_l150_m2_e1 | het | 50.5495 | 48.9362 | 52.2727 | 95.2586 | 23 | 24 | 23 | 21 | 4 | 19.0476 | |
| ciseli-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 35.4839 | 31.4286 | 40.7407 | 83.1250 | 11 | 24 | 11 | 16 | 15 | 93.7500 | |
| ciseli-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 18.7500 | 11.1111 | 60.0000 | 95.6522 | 3 | 24 | 3 | 2 | 1 | 50.0000 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 8.0000 | 11.1111 | 6.2500 | 76.8116 | 3 | 24 | 1 | 15 | 0 | 0.0000 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 33.1579 | 52.9412 | 24.1379 | 86.1022 | 27 | 24 | 21 | 66 | 2 | 3.0303 | |
| ciseli-custom | INDEL | I6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 56.5463 | 51.0204 | 63.4146 | 78.6458 | 25 | 24 | 26 | 15 | 14 | 93.3333 | |
| ciseli-custom | INDEL | I6_15 | map_l150_m2_e1 | * | 18.7500 | 11.1111 | 60.0000 | 97.2973 | 3 | 24 | 3 | 2 | 1 | 50.0000 | |
| cchapple-custom | INDEL | D1_5 | map_l150_m2_e0 | * | 95.7666 | 96.8545 | 94.7028 | 87.9645 | 739 | 24 | 733 | 41 | 6 | 14.6341 | |
| cchapple-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 0.0000 | 92.9619 | 0.0000 | 0.0000 | 317 | 24 | 0 | 0 | 0 | ||
| cchapple-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 0.0000 | 93.6842 | 0.0000 | 0.0000 | 356 | 24 | 0 | 0 | 0 | ||
| ciseli-custom | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 96.5171 | 99.1298 | 94.0386 | 44.7974 | 2734 | 24 | 2729 | 173 | 47 | 27.1676 | |
| ciseli-custom | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 96.7631 | 99.4231 | 94.2417 | 48.2590 | 3964 | 23 | 3977 | 243 | 84 | 34.5679 | |
| ciseli-custom | SNP | tv | func_cds | * | 95.2555 | 99.4738 | 91.3804 | 30.2616 | 4348 | 23 | 4336 | 409 | 11 | 2.6895 | |
| ciseli-custom | SNP | tv | segdup | homalt | 97.7133 | 99.2897 | 96.1862 | 90.1152 | 3215 | 23 | 3203 | 127 | 72 | 56.6929 | |
| ckim-dragen | INDEL | D1_5 | map_l100_m0_e0 | * | 96.8796 | 97.3349 | 96.4286 | 86.1120 | 840 | 23 | 837 | 31 | 4 | 12.9032 | |
| ckim-dragen | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.8216 | 96.0549 | 99.6546 | 66.2784 | 560 | 23 | 577 | 2 | 2 | 100.0000 | |
| ckim-dragen | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 96.6296 | 93.9474 | 99.4695 | 63.7151 | 357 | 23 | 375 | 2 | 2 | 100.0000 | |
| ckim-dragen | INDEL | I1_5 | map_l150_m1_e0 | het | 93.5679 | 92.3077 | 94.8630 | 91.0374 | 276 | 23 | 277 | 15 | 2 | 13.3333 | |
| ckim-dragen | INDEL | I1_5 | map_l150_m2_e0 | het | 93.7785 | 92.5566 | 95.0331 | 91.9659 | 286 | 23 | 287 | 15 | 2 | 13.3333 | |
| ckim-dragen | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.0173 | 98.5075 | 99.5324 | 77.0540 | 1518 | 23 | 1490 | 7 | 3 | 42.8571 | |
| ckim-dragen | SNP | tv | HG002compoundhet | * | 99.7984 | 99.7422 | 99.8546 | 49.3913 | 8900 | 23 | 8925 | 13 | 8 | 61.5385 | |
| ckim-dragen | SNP | tv | map_l150_m1_e0 | homalt | 99.5559 | 99.4171 | 99.6950 | 66.7792 | 3923 | 23 | 3923 | 12 | 10 | 83.3333 | |
| ckim-dragen | SNP | tv | map_l150_m2_e0 | homalt | 99.5708 | 99.4367 | 99.7053 | 69.4134 | 4060 | 23 | 4060 | 12 | 10 | 83.3333 | |
| ckim-dragen | SNP | tv | map_l150_m2_e1 | homalt | 99.5761 | 99.4436 | 99.7089 | 69.3912 | 4111 | 23 | 4111 | 12 | 10 | 83.3333 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 97.8966 | 96.4615 | 99.3750 | 22.2357 | 627 | 23 | 636 | 4 | 4 | 100.0000 | |
| ckim-gatk | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 97.2012 | 96.5257 | 97.8862 | 78.6532 | 639 | 23 | 602 | 13 | 7 | 53.8462 | |