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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
65401-65450 / 86044 show all | |||||||||||||||
| jli-custom | INDEL | * | map_l150_m2_e0 | het | 98.1776 | 98.0132 | 98.3425 | 89.4239 | 888 | 18 | 890 | 15 | 4 | 26.6667 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 93.2615 | 97.1904 | 89.6378 | 74.6299 | 934 | 27 | 891 | 103 | 93 | 90.2913 | |
| asubramanian-gatk | SNP | tv | map_l100_m0_e0 | homalt | 37.6187 | 23.1669 | 100.0000 | 87.8146 | 891 | 2955 | 891 | 0 | 0 | ||
| hfeng-pmm3 | INDEL | * | map_l150_m2_e0 | het | 97.9638 | 98.0132 | 97.9144 | 88.9709 | 888 | 18 | 892 | 19 | 3 | 15.7895 | |
| gduggal-bwavard | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 55.0595 | 38.1013 | 99.2214 | 43.7774 | 903 | 1467 | 892 | 7 | 6 | 85.7143 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 94.7289 | 93.1818 | 96.3283 | 76.7629 | 902 | 66 | 892 | 34 | 8 | 23.5294 | |
| jpowers-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 91.6782 | 96.9631 | 86.9396 | 76.4300 | 894 | 28 | 892 | 134 | 128 | 95.5224 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 96.6005 | 95.5255 | 97.6999 | 63.9558 | 918 | 43 | 892 | 21 | 10 | 47.6190 | |
| ckim-dragen | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 96.3915 | 97.1904 | 95.6056 | 75.0334 | 934 | 27 | 892 | 41 | 38 | 92.6829 | |
| ckim-dragen | SNP | ti | map_l250_m0_e0 | het | 95.1974 | 95.5032 | 94.8936 | 94.2165 | 892 | 42 | 892 | 48 | 1 | 2.0833 | |
| dgrover-gatk | INDEL | * | map_l150_m2_e0 | het | 97.8027 | 98.0132 | 97.5930 | 91.8342 | 888 | 18 | 892 | 22 | 3 | 13.6364 | |
| jmaeng-gatk | INDEL | * | map_l150_m2_e0 | het | 94.5436 | 98.1236 | 91.2155 | 94.1716 | 889 | 17 | 893 | 86 | 6 | 6.9767 | |
| jlack-gatk | INDEL | * | map_l150_m2_e0 | het | 91.3052 | 98.1236 | 85.3728 | 93.4833 | 889 | 17 | 893 | 153 | 6 | 3.9216 | |
| gduggal-bwaplat | INDEL | D1_5 | map_l100_m1_e0 | het | 84.4444 | 73.8627 | 98.5651 | 92.5841 | 893 | 316 | 893 | 13 | 4 | 30.7692 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 81.2972 | 84.9765 | 77.9232 | 58.9542 | 905 | 160 | 893 | 253 | 210 | 83.0040 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.1871 | 95.2331 | 99.2231 | 35.3659 | 899 | 45 | 894 | 7 | 7 | 100.0000 | |
| ltrigg-rtg1 | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 96.5497 | 95.4214 | 97.7049 | 66.6424 | 917 | 44 | 894 | 21 | 10 | 47.6190 | |
| raldana-dualsentieon | INDEL | * | map_l150_m2_e1 | het | 96.9025 | 96.3203 | 97.4918 | 88.7346 | 890 | 34 | 894 | 23 | 2 | 8.6957 | |
| mlin-fermikit | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.0055 | 98.0306 | 100.0000 | 65.5504 | 896 | 18 | 895 | 0 | 0 | ||
| ckim-isaac | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 78.3824 | 64.7764 | 99.2239 | 34.3044 | 811 | 441 | 895 | 7 | 4 | 57.1429 | |
| jmaeng-gatk | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 98.2940 | 96.7497 | 99.8884 | 27.0952 | 893 | 30 | 895 | 1 | 1 | 100.0000 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 73.6947 | 65.2837 | 84.5936 | 37.0238 | 771 | 410 | 895 | 163 | 163 | 100.0000 | |
| gduggal-bwavard | INDEL | * | map_l150_m2_e0 | het | 88.9752 | 98.5651 | 81.0860 | 93.2486 | 893 | 13 | 896 | 209 | 44 | 21.0526 | |
| qzeng-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 91.7867 | 95.1821 | 88.6251 | 90.1491 | 810 | 41 | 896 | 115 | 26 | 22.6087 | |
| qzeng-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 98.6811 | 99.6718 | 97.7099 | 74.8698 | 911 | 3 | 896 | 21 | 0 | 0.0000 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 83.1246 | 82.0664 | 84.2105 | 65.4096 | 1112 | 243 | 896 | 168 | 107 | 63.6905 | |
| bgallagher-sentieon | INDEL | * | map_l150_m2_e0 | het | 97.6001 | 98.4547 | 96.7603 | 91.1986 | 892 | 14 | 896 | 30 | 4 | 13.3333 | |
| hfeng-pmm2 | INDEL | * | map_l150_m2_e0 | het | 97.4409 | 98.4547 | 96.4478 | 90.9902 | 892 | 14 | 896 | 33 | 3 | 9.0909 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 95.3619 | 93.9050 | 96.8649 | 73.4043 | 909 | 59 | 896 | 29 | 7 | 24.1379 | |
| cchapple-custom | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 98.9542 | 98.7939 | 99.1150 | 59.1505 | 901 | 11 | 896 | 8 | 8 | 100.0000 | |
| ckim-gatk | INDEL | * | map_l150_m2_e0 | het | 94.2693 | 98.5651 | 90.3323 | 93.9690 | 893 | 13 | 897 | 96 | 6 | 6.2500 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 39.4885 | 37.0800 | 42.2316 | 61.7642 | 894 | 1517 | 897 | 1227 | 722 | 58.8427 | |
| gduggal-snapvard | INDEL | * | map_l125_m2_e1 | homalt | 92.3972 | 86.9509 | 98.5714 | 81.2719 | 673 | 101 | 897 | 13 | 11 | 84.6154 | |
| ghariani-varprowl | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 92.6592 | 93.9050 | 91.4460 | 61.1858 | 909 | 59 | 898 | 84 | 35 | 41.6667 | |
| asubramanian-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 98.0755 | 97.3713 | 98.7899 | 89.5852 | 889 | 24 | 898 | 11 | 9 | 81.8182 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 68.4973 | 52.5761 | 98.2495 | 47.4411 | 898 | 810 | 898 | 16 | 15 | 93.7500 | |
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 80.9237 | 76.2066 | 86.2632 | 43.6078 | 900 | 281 | 898 | 143 | 143 | 100.0000 | |
| rpoplin-dv42 | INDEL | * | map_l150_m2_e1 | het | 97.5486 | 96.7532 | 98.3571 | 89.4487 | 894 | 30 | 898 | 15 | 6 | 40.0000 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 81.1064 | 76.2066 | 86.6795 | 41.5020 | 900 | 281 | 898 | 138 | 138 | 100.0000 | |
| ckim-gatk | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 98.4617 | 97.0748 | 99.8889 | 26.7101 | 896 | 27 | 899 | 1 | 1 | 100.0000 | |
| mlin-fermikit | INDEL | * | map_l100_m1_e0 | homalt | 76.5877 | 73.3496 | 80.1248 | 79.4844 | 900 | 327 | 899 | 223 | 196 | 87.8924 | |
| ckim-vqsr | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 98.4617 | 97.0748 | 99.8889 | 26.7101 | 896 | 27 | 899 | 1 | 1 | 100.0000 | |
| gduggal-bwaplat | INDEL | I6_15 | HG002complexvar | hetalt | 84.1254 | 73.6713 | 98.0371 | 62.0604 | 901 | 322 | 899 | 18 | 17 | 94.4444 | |
| gduggal-snapfb | INDEL | * | segdup | homalt | 95.2260 | 93.4375 | 97.0842 | 94.2949 | 897 | 63 | 899 | 27 | 15 | 55.5556 | |
| jpowers-varprowl | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 80.1588 | 67.7444 | 98.1441 | 38.0663 | 901 | 429 | 899 | 17 | 16 | 94.1176 | |
| jmaeng-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 98.9011 | 98.5761 | 99.2282 | 89.6010 | 900 | 13 | 900 | 7 | 6 | 85.7143 | |
| ghariani-varprowl | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 80.1595 | 67.7444 | 98.1461 | 38.4977 | 901 | 429 | 900 | 17 | 15 | 88.2353 | |
| gduggal-snapvard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 61.8951 | 85.0543 | 48.6486 | 86.3559 | 939 | 165 | 900 | 950 | 47 | 4.9474 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 77.8072 | 93.6126 | 66.5680 | 74.1046 | 894 | 61 | 900 | 452 | 50 | 11.0619 | |
| cchapple-custom | SNP | tv | map_l250_m2_e0 | homalt | 97.9858 | 96.0512 | 100.0000 | 85.3349 | 900 | 37 | 900 | 0 | 0 | ||