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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
13901-13950 / 86044 show all | |||||||||||||||
| ckim-vqsr | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.6913 | 98.9362 | 92.6526 | 62.3535 | 744 | 8 | 744 | 59 | 58 | 98.3051 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 83.9050 | 98.7578 | 72.9358 | 36.8116 | 159 | 2 | 159 | 59 | 59 | 100.0000 | |
| ckim-vqsr | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.3373 | 95.6976 | 99.0342 | 63.1411 | 6050 | 272 | 6050 | 59 | 49 | 83.0508 | |
| ckim-vqsr | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.3373 | 95.6976 | 99.0342 | 63.1411 | 6050 | 272 | 6050 | 59 | 49 | 83.0508 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 98.7701 | 99.9578 | 97.6102 | 56.2071 | 2369 | 1 | 2369 | 58 | 57 | 98.2759 | |
| egarrison-hhga | SNP | * | map_l150_m2_e0 | het | 99.1156 | 98.5298 | 99.7085 | 75.6800 | 19837 | 296 | 19837 | 58 | 22 | 37.9310 | |
| egarrison-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.2233 | 97.8292 | 98.6207 | 80.5008 | 4146 | 92 | 4147 | 58 | 16 | 27.5862 | |
| egarrison-hhga | SNP | ti | map_l100_m2_e1 | het | 99.3984 | 98.9890 | 99.8111 | 65.4651 | 30647 | 313 | 30648 | 58 | 18 | 31.0345 | |
| eyeh-varpipe | INDEL | * | map_l150_m2_e0 | * | 96.5842 | 96.1648 | 97.0072 | 95.5563 | 1354 | 54 | 1880 | 58 | 41 | 70.6897 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.6427 | 99.5150 | 99.7707 | 54.4892 | 25236 | 123 | 25236 | 58 | 45 | 77.5862 | |
| dgrover-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.7354 | 96.2302 | 99.2883 | 62.1142 | 8092 | 317 | 8092 | 58 | 49 | 84.4828 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.8137 | 96.5992 | 99.0592 | 63.6797 | 6107 | 215 | 6107 | 58 | 48 | 82.7586 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.8137 | 96.5992 | 99.0592 | 63.6797 | 6107 | 215 | 6107 | 58 | 48 | 82.7586 | |
| egarrison-hhga | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | * | 71.7925 | 70.7207 | 72.8972 | 84.2415 | 157 | 65 | 156 | 58 | 51 | 87.9310 | |
| egarrison-hhga | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | het | 56.0000 | 84.0000 | 42.0000 | 67.7419 | 42 | 8 | 42 | 58 | 51 | 87.9310 | |
| dgrover-gatk | INDEL | * | map_siren | het | 98.8042 | 98.8909 | 98.7177 | 84.1153 | 4458 | 50 | 4465 | 58 | 7 | 12.0690 | |
| ghariani-varprowl | INDEL | I1_5 | map_l125_m2_e0 | * | 94.2808 | 95.2159 | 93.3638 | 89.9679 | 816 | 41 | 816 | 58 | 21 | 36.2069 | |
| ghariani-varprowl | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 42.3077 | 35.1064 | 53.2258 | 74.8988 | 66 | 122 | 66 | 58 | 49 | 84.4828 | |
| ghariani-varprowl | SNP | * | map_l125_m1_e0 | homalt | 99.0868 | 98.5271 | 99.6530 | 67.5166 | 16656 | 249 | 16656 | 58 | 39 | 67.2414 | |
| ghariani-varprowl | SNP | * | map_l125_m2_e0 | homalt | 99.1058 | 98.5554 | 99.6624 | 70.0500 | 17124 | 251 | 17124 | 58 | 39 | 67.2414 | |
| ghariani-varprowl | SNP | * | map_l125_m2_e1 | homalt | 99.1110 | 98.5626 | 99.6655 | 70.0625 | 17280 | 252 | 17280 | 58 | 39 | 67.2414 | |
| ghariani-varprowl | SNP | ti | segdup | homalt | 99.5818 | 99.9334 | 99.2326 | 88.7647 | 7500 | 5 | 7500 | 58 | 36 | 62.0690 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 69.3384 | 66.5414 | 72.3810 | 85.5372 | 177 | 89 | 152 | 58 | 39 | 67.2414 | |
| gduggal-snapplat | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 42.3946 | 28.6024 | 81.8750 | 58.3875 | 264 | 659 | 262 | 58 | 51 | 87.9310 | |
| gduggal-snapplat | INDEL | * | map_l150_m0_e0 | * | 78.7001 | 71.7899 | 87.0824 | 96.1959 | 369 | 145 | 391 | 58 | 10 | 17.2414 | |
| gduggal-snapplat | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 89.0395 | 80.9340 | 98.9493 | 51.2411 | 5459 | 1286 | 5462 | 58 | 26 | 44.8276 | |
| gduggal-bwaplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 69.2265 | 56.5217 | 89.2989 | 95.0257 | 481 | 370 | 484 | 58 | 10 | 17.2414 | |
| gduggal-bwaplat | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | het | 91.5844 | 85.2017 | 99.0009 | 65.9710 | 5746 | 998 | 5747 | 58 | 17 | 29.3103 | |
| eyeh-varpipe | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 72.7749 | 91.8182 | 60.2740 | 84.1649 | 101 | 9 | 88 | 58 | 16 | 27.5862 | |
| gduggal-bwavard | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 68.4211 | 64.4628 | 72.8972 | 66.9243 | 156 | 86 | 156 | 58 | 55 | 94.8276 | |
| gduggal-bwavard | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 78.6395 | 95.0820 | 67.0455 | 69.1769 | 116 | 6 | 118 | 58 | 55 | 94.8276 | |
| eyeh-varpipe | INDEL | D1_5 | map_l100_m1_e0 | * | 97.0472 | 96.6450 | 97.4528 | 83.5060 | 1786 | 62 | 2219 | 58 | 35 | 60.3448 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_51to200 | * | 29.7872 | 24.6479 | 37.6344 | 33.0935 | 35 | 107 | 35 | 58 | 57 | 98.2759 | |
| gduggal-bwafb | SNP | tv | map_l250_m1_e0 | het | 96.5517 | 96.3626 | 96.7416 | 89.4306 | 1722 | 65 | 1722 | 58 | 11 | 18.9655 | |
| ckim-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.2264 | 95.2551 | 99.2811 | 61.5901 | 8010 | 399 | 8010 | 58 | 49 | 84.4828 | |
| ckim-gatk | SNP | tv | map_l250_m2_e0 | * | 69.3914 | 54.1985 | 96.4198 | 96.4303 | 1562 | 1320 | 1562 | 58 | 1 | 1.7241 | |
| ckim-gatk | SNP | tv | map_l250_m2_e0 | het | 72.7389 | 58.8660 | 95.1667 | 96.8726 | 1142 | 798 | 1142 | 58 | 1 | 1.7241 | |
| ckim-dragen | SNP | ti | * | homalt | 99.9710 | 99.9493 | 99.9928 | 15.7227 | 802631 | 407 | 802738 | 58 | 51 | 87.9310 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 98.7701 | 99.9578 | 97.6102 | 56.2071 | 2369 | 1 | 2369 | 58 | 57 | 98.2759 | |
| ciseli-custom | SNP | * | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 49.5193 | 78.0488 | 36.2637 | 92.4606 | 32 | 9 | 33 | 58 | 18 | 31.0345 | |
| ckim-dragen | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.2357 | 94.9731 | 99.6087 | 58.9389 | 14642 | 775 | 14763 | 58 | 58 | 100.0000 | |
| cchapple-custom | SNP | * | * | homalt | 99.9445 | 99.8940 | 99.9951 | 16.2464 | 1178910 | 1251 | 1177636 | 58 | 51 | 87.9310 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.1075 | 96.6926 | 99.5645 | 63.4833 | 13302 | 455 | 13260 | 58 | 44 | 75.8621 | |
| hfeng-pmm3 | SNP | tv | map_l100_m0_e0 | * | 99.4268 | 99.3775 | 99.4762 | 69.0933 | 11015 | 69 | 11014 | 58 | 8 | 13.7931 | |
| hfeng-pmm2 | SNP | * | map_l250_m0_e0 | * | 97.8575 | 98.4075 | 97.3136 | 93.5175 | 2101 | 34 | 2101 | 58 | 9 | 15.5172 | |
| hfeng-pmm2 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.2678 | 97.2079 | 99.3509 | 74.1300 | 8878 | 255 | 8878 | 58 | 4 | 6.8966 | |
| hfeng-pmm2 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.2678 | 97.2079 | 99.3509 | 74.1300 | 8878 | 255 | 8878 | 58 | 4 | 6.8966 | |
| hfeng-pmm3 | INDEL | D1_5 | * | homalt | 99.8825 | 99.8835 | 99.8815 | 58.1721 | 48869 | 57 | 48874 | 58 | 56 | 96.5517 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.1075 | 96.6926 | 99.5645 | 63.4833 | 13302 | 455 | 13260 | 58 | 44 | 75.8621 | |
| jlack-gatk | INDEL | I1_5 | map_l100_m1_e0 | het | 95.4470 | 98.0695 | 92.9612 | 88.8271 | 762 | 15 | 766 | 58 | 3 | 5.1724 | |