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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
62851-62900 / 86044 show all | |||||||||||||||
| qzeng-custom | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 61.8683 | 67.3684 | 57.1984 | 66.9241 | 64 | 31 | 147 | 110 | 43 | 39.0909 | |
| raldana-dualsentieon | INDEL | * | map_l150_m1_e0 | het | 96.8336 | 96.3743 | 97.2973 | 87.9068 | 824 | 31 | 828 | 23 | 2 | 8.6957 | |
| ndellapenna-hhga | INDEL | * | map_l100_m2_e0 | hetalt | 83.7547 | 75.2000 | 94.5055 | 89.4798 | 94 | 31 | 86 | 5 | 2 | 40.0000 | |
| ltrigg-rtg2 | INDEL | D1_5 | map_l100_m0_e0 | * | 97.7664 | 96.4079 | 99.1637 | 75.6190 | 832 | 31 | 830 | 7 | 1 | 14.2857 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.8577 | 98.8657 | 98.8497 | 50.4413 | 2702 | 31 | 2664 | 31 | 15 | 48.3871 | |
| ltrigg-rtg2 | SNP | * | map_l150_m0_e0 | homalt | 99.5584 | 99.2419 | 99.8769 | 71.8698 | 4058 | 31 | 4057 | 5 | 4 | 80.0000 | |
| mlin-fermikit | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 86.6742 | 85.1675 | 88.2353 | 70.5628 | 178 | 31 | 180 | 24 | 21 | 87.5000 | |
| mlin-fermikit | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | het | 92.3787 | 95.5903 | 89.3758 | 38.2787 | 672 | 31 | 673 | 80 | 79 | 98.7500 | |
| mlin-fermikit | INDEL | D6_15 | map_l100_m1_e0 | het | 75.2952 | 75.3968 | 75.1938 | 79.7488 | 95 | 31 | 97 | 32 | 23 | 71.8750 | |
| mlin-fermikit | INDEL | D6_15 | map_l100_m2_e0 | het | 76.2275 | 76.3359 | 76.1194 | 81.1001 | 100 | 31 | 102 | 32 | 23 | 71.8750 | |
| mlin-fermikit | INDEL | D6_15 | map_l100_m2_e1 | het | 76.0958 | 77.0370 | 75.1773 | 80.9202 | 104 | 31 | 106 | 35 | 25 | 71.4286 | |
| mlin-fermikit | INDEL | D6_15 | segdup | * | 86.7731 | 83.7696 | 90.0000 | 91.8182 | 160 | 31 | 162 | 18 | 17 | 94.4444 | |
| mlin-fermikit | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 73.7321 | 76.6917 | 70.9924 | 82.6490 | 102 | 31 | 93 | 38 | 38 | 100.0000 | |
| mlin-fermikit | SNP | ti | * | hetalt | 97.1781 | 94.6735 | 99.8188 | 32.3529 | 551 | 31 | 551 | 1 | 1 | 100.0000 | |
| mlin-fermikit | SNP | ti | HG002compoundhet | hetalt | 97.2493 | 94.6459 | 100.0000 | 20.8092 | 548 | 31 | 548 | 0 | 0 | ||
| anovak-vg | SNP | ti | lowcmp_SimpleRepeat_quadTR_51to200 | * | 61.5814 | 69.3069 | 55.4054 | 91.6337 | 70 | 31 | 82 | 66 | 26 | 39.3939 | |
| anovak-vg | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 97.9774 | 97.8472 | 98.1079 | 69.1926 | 1409 | 31 | 1400 | 27 | 11 | 40.7407 | |
| astatham-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 97.8006 | 97.5318 | 98.0707 | 78.8291 | 1225 | 31 | 1220 | 24 | 7 | 29.1667 | |
| anovak-vg | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | hetalt | 0.0000 | 20.5128 | 0.0000 | 0.0000 | 8 | 31 | 0 | 0 | 0 | ||
| anovak-vg | INDEL | D6_15 | map_l125_m1_e0 | * | 75.8631 | 73.5043 | 78.3784 | 88.8554 | 86 | 31 | 87 | 24 | 15 | 62.5000 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 96.2794 | 95.8165 | 96.7468 | 75.0088 | 710 | 31 | 684 | 23 | 20 | 86.9565 | |
| bgallagher-sentieon | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 94.9615 | 90.9091 | 99.3921 | 58.2487 | 310 | 31 | 327 | 2 | 2 | 100.0000 | |
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 78.7097 | 66.3043 | 96.8254 | 60.1266 | 61 | 31 | 61 | 2 | 1 | 50.0000 | |
| bgallagher-sentieon | SNP | ti | HG002compoundhet | * | 99.8512 | 99.8226 | 99.8798 | 35.5355 | 17447 | 31 | 17445 | 21 | 14 | 66.6667 | |
| bgallagher-sentieon | SNP | tv | map_l100_m1_e0 | homalt | 99.7786 | 99.6572 | 99.9002 | 59.2105 | 9012 | 31 | 9012 | 9 | 6 | 66.6667 | |
| bgallagher-sentieon | SNP | tv | map_l100_m2_e0 | homalt | 99.7827 | 99.6636 | 99.9021 | 61.6697 | 9183 | 31 | 9183 | 9 | 6 | 66.6667 | |
| bgallagher-sentieon | SNP | tv | map_l100_m2_e1 | homalt | 99.7847 | 99.6667 | 99.9030 | 61.6624 | 9271 | 31 | 9271 | 9 | 6 | 66.6667 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 98.5824 | 99.3478 | 97.8288 | 50.3389 | 4722 | 31 | 4731 | 105 | 95 | 90.4762 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.8131 | 99.6954 | 99.9311 | 54.3062 | 10147 | 31 | 10148 | 7 | 7 | 100.0000 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.5939 | 99.2396 | 99.9506 | 44.1181 | 4046 | 31 | 4050 | 2 | 1 | 50.0000 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 96.7581 | 95.3172 | 98.2432 | 76.2972 | 631 | 31 | 727 | 13 | 8 | 61.5385 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 98.5686 | 97.2591 | 99.9139 | 42.5606 | 1100 | 31 | 1161 | 1 | 0 | 0.0000 | |
| asubramanian-gatk | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.2697 | 98.7490 | 99.7960 | 33.5412 | 2447 | 31 | 2446 | 5 | 0 | 0.0000 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 99.0900 | 99.5359 | 98.6480 | 56.8443 | 6648 | 31 | 6640 | 91 | 88 | 96.7033 | |
| astatham-gatk | INDEL | D1_5 | map_l150_m2_e1 | * | 96.5155 | 96.0154 | 97.0207 | 90.1102 | 747 | 31 | 749 | 23 | 5 | 21.7391 | |
| astatham-gatk | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 95.3320 | 93.5417 | 97.1922 | 82.4555 | 449 | 31 | 450 | 13 | 12 | 92.3077 | |
| cchapple-custom | INDEL | I1_5 | map_l125_m2_e0 | * | 96.8251 | 96.3827 | 97.2716 | 86.3349 | 826 | 31 | 820 | 23 | 6 | 26.0870 | |
| cchapple-custom | INDEL | I1_5 | map_l125_m2_e1 | * | 96.8730 | 96.4368 | 97.3131 | 86.4514 | 839 | 31 | 833 | 23 | 6 | 26.0870 | |
| cchapple-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 97.3086 | 96.6046 | 98.0229 | 87.6589 | 882 | 31 | 942 | 19 | 9 | 47.3684 | |
| cchapple-custom | SNP | tv | map_l250_m0_e0 | het | 93.7547 | 94.5804 | 92.9432 | 94.2561 | 541 | 31 | 540 | 41 | 8 | 19.5122 | |
| ckim-dragen | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.8273 | 99.7901 | 99.8645 | 55.6157 | 14739 | 31 | 14740 | 20 | 5 | 25.0000 | |
| ckim-dragen | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.9169 | 99.3027 | 98.5341 | 69.1612 | 4415 | 31 | 4369 | 65 | 62 | 95.3846 | |
| ckim-dragen | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 96.8266 | 95.4876 | 98.2036 | 81.6484 | 656 | 31 | 656 | 12 | 10 | 83.3333 | |
| ckim-dragen | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 98.6105 | 97.2591 | 100.0000 | 41.6754 | 1100 | 31 | 1107 | 0 | 0 | ||
| ckim-dragen | INDEL | I1_5 | map_l125_m1_e0 | * | 96.6727 | 96.2651 | 97.0838 | 86.5742 | 799 | 31 | 799 | 24 | 6 | 25.0000 | |
| ckim-dragen | INDEL | I1_5 | map_l125_m2_e0 | * | 96.7213 | 96.3827 | 97.0623 | 87.8080 | 826 | 31 | 826 | 25 | 6 | 24.0000 | |
| ckim-dragen | INDEL | I1_5 | map_l125_m2_e1 | * | 96.7147 | 96.4368 | 96.9942 | 87.9173 | 839 | 31 | 839 | 26 | 6 | 23.0769 | |
| ckim-dragen | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 99.7268 | 99.6801 | 99.7735 | 67.9777 | 9661 | 31 | 9691 | 22 | 18 | 81.8182 | |
| ckim-dragen | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 98.7983 | 98.3069 | 99.2946 | 51.3464 | 1800 | 31 | 1830 | 13 | 2 | 15.3846 | |
| ckim-dragen | SNP | tv | map_l250_m0_e0 | * | 95.6975 | 95.9477 | 95.4486 | 93.6441 | 734 | 31 | 734 | 35 | 5 | 14.2857 | |