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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
38201-38250 / 86044 show all | |||||||||||||||
| ckim-vqsr | INDEL | * | map_l250_m0_e0 | het | 83.6066 | 96.2264 | 73.9130 | 98.5907 | 51 | 2 | 51 | 18 | 0 | 0.0000 | |
| cchapple-custom | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_51to200 | het | 83.6066 | 75.0000 | 94.4444 | 59.5506 | 6 | 2 | 34 | 2 | 2 | 100.0000 | |
| bgallagher-sentieon | INDEL | I16_PLUS | HG002compoundhet | het | 83.6026 | 95.7447 | 74.1935 | 93.6735 | 45 | 2 | 23 | 8 | 8 | 100.0000 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 83.6015 | 87.3211 | 80.1860 | 72.6837 | 13602 | 1975 | 12246 | 3026 | 728 | 24.0582 | |
| gduggal-bwaplat | INDEL | D6_15 | HG002complexvar | * | 83.5998 | 73.9721 | 96.1087 | 66.0264 | 3922 | 1380 | 3927 | 159 | 104 | 65.4088 | |
| mlin-fermikit | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 83.5892 | 71.9405 | 99.7391 | 27.4753 | 3433 | 1339 | 3441 | 9 | 9 | 100.0000 | |
| gduggal-snapvard | SNP | tv | map_l150_m0_e0 | het | 83.5823 | 96.6936 | 73.6022 | 87.1311 | 2749 | 94 | 2738 | 982 | 41 | 4.1752 | |
| qzeng-custom | INDEL | * | map_l100_m2_e0 | het | 83.5804 | 79.9740 | 87.5274 | 89.7430 | 1845 | 462 | 2400 | 342 | 54 | 15.7895 | |
| gduggal-bwaplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 83.5790 | 73.7247 | 96.4741 | 64.8422 | 23586 | 8406 | 23586 | 862 | 511 | 59.2807 | |
| qzeng-custom | SNP | tv | map_l150_m2_e0 | het | 83.5782 | 74.2554 | 95.5781 | 89.7806 | 5385 | 1867 | 5382 | 249 | 204 | 81.9277 | |
| gduggal-bwavard | INDEL | * | map_l250_m2_e1 | * | 83.5781 | 93.9940 | 75.2404 | 96.4341 | 313 | 20 | 313 | 103 | 15 | 14.5631 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 83.5759 | 89.6241 | 78.2925 | 40.0872 | 1192 | 138 | 1183 | 328 | 283 | 86.2805 | |
| gduggal-bwaplat | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 83.5750 | 73.9861 | 96.0194 | 60.2412 | 27073 | 9519 | 27065 | 1122 | 616 | 54.9020 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 83.5727 | 82.8140 | 84.3455 | 36.4989 | 15121 | 3138 | 15194 | 2820 | 2630 | 93.2624 | |
| gduggal-snapplat | INDEL | D1_5 | map_l150_m1_e0 | het | 83.5667 | 80.4979 | 86.8787 | 94.5219 | 388 | 94 | 437 | 66 | 17 | 25.7576 | |
| ndellapenna-hhga | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | * | 83.5594 | 82.2599 | 84.9006 | 82.0181 | 2184 | 471 | 2221 | 395 | 339 | 85.8228 | |
| gduggal-snapplat | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 83.5589 | 88.9822 | 78.7587 | 90.6848 | 1801 | 223 | 1802 | 486 | 14 | 2.8807 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 83.5587 | 94.3683 | 74.9709 | 75.2021 | 620 | 37 | 644 | 215 | 21 | 9.7674 | |
| ciseli-custom | INDEL | D1_5 | map_l100_m1_e0 | homalt | 83.5566 | 85.6419 | 81.5705 | 83.0803 | 507 | 85 | 509 | 115 | 98 | 85.2174 | |
| ciseli-custom | INDEL | * | * | * | 83.5453 | 82.5314 | 84.5844 | 60.0787 | 284352 | 60186 | 284718 | 51890 | 36584 | 70.5030 | |
| anovak-vg | SNP | ti | tech_badpromoters | het | 83.5443 | 75.0000 | 94.2857 | 45.3125 | 33 | 11 | 33 | 2 | 2 | 100.0000 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 83.5380 | 73.1417 | 97.3796 | 64.9640 | 10814 | 3971 | 10814 | 291 | 228 | 78.3505 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 83.5360 | 76.8142 | 91.5470 | 43.3092 | 2117 | 639 | 2296 | 212 | 212 | 100.0000 | |
| gduggal-snapplat | INDEL | * | map_l100_m0_e0 | homalt | 83.5293 | 73.6739 | 96.4286 | 89.2418 | 375 | 134 | 405 | 15 | 1 | 6.6667 | |
| gduggal-snapfb | INDEL | D6_15 | map_l150_m2_e1 | het | 83.5267 | 76.5957 | 91.8367 | 83.1034 | 36 | 11 | 45 | 4 | 3 | 75.0000 | |
| ltrigg-rtg1 | SNP | * | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 83.5267 | 73.1707 | 97.2973 | 89.3372 | 30 | 11 | 36 | 1 | 1 | 100.0000 | |
| hfeng-pmm1 | INDEL | I1_5 | HG002compoundhet | homalt | 83.5249 | 99.3921 | 72.0264 | 83.4186 | 327 | 2 | 327 | 127 | 126 | 99.2126 | |
| asubramanian-gatk | INDEL | I6_15 | HG002compoundhet | het | 83.5162 | 93.2692 | 75.6098 | 84.8597 | 194 | 14 | 155 | 50 | 46 | 92.0000 | |
| ciseli-custom | INDEL | D1_5 | map_siren | het | 83.5161 | 80.9398 | 86.2617 | 86.1336 | 1843 | 434 | 1846 | 294 | 66 | 22.4490 | |
| mlin-fermikit | INDEL | I1_5 | map_siren | * | 83.5106 | 74.6755 | 94.7168 | 75.2199 | 2244 | 761 | 2241 | 125 | 111 | 88.8000 | |
| eyeh-varpipe | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 83.5091 | 84.3949 | 82.6418 | 67.4764 | 1060 | 196 | 1195 | 251 | 203 | 80.8765 | |
| gduggal-bwavard | INDEL | * | map_l250_m2_e0 | * | 83.4899 | 93.9577 | 75.1208 | 96.3544 | 311 | 20 | 311 | 103 | 15 | 14.5631 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 83.4868 | 81.5589 | 85.5080 | 68.6930 | 3317 | 750 | 3316 | 562 | 522 | 92.8826 | |
| qzeng-custom | SNP | * | map_l125_m1_e0 | * | 83.4865 | 72.9742 | 97.5374 | 82.2302 | 33077 | 12250 | 32716 | 826 | 701 | 84.8668 | |
| eyeh-varpipe | INDEL | I1_5 | map_l125_m2_e0 | hetalt | 83.4862 | 73.6842 | 96.2963 | 92.3944 | 14 | 5 | 26 | 1 | 0 | 0.0000 | |
| eyeh-varpipe | INDEL | I1_5 | map_l125_m2_e1 | hetalt | 83.4862 | 73.6842 | 96.2963 | 92.5000 | 14 | 5 | 26 | 1 | 0 | 0.0000 | |
| eyeh-varpipe | INDEL | I6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 83.4783 | 85.7143 | 81.3559 | 70.4013 | 42 | 7 | 144 | 33 | 30 | 90.9091 | |
| gduggal-bwavard | INDEL | D6_15 | map_l100_m2_e1 | homalt | 83.4783 | 71.6418 | 100.0000 | 81.0924 | 48 | 19 | 45 | 0 | 0 | ||
| ckim-isaac | INDEL | I1_5 | map_l100_m1_e0 | hetalt | 83.4783 | 75.0000 | 94.1176 | 87.1698 | 33 | 11 | 32 | 2 | 2 | 100.0000 | |
| ckim-isaac | INDEL | I1_5 | map_l100_m2_e0 | hetalt | 83.4783 | 75.0000 | 94.1176 | 88.4354 | 33 | 11 | 32 | 2 | 2 | 100.0000 | |
| gduggal-bwaplat | INDEL | D6_15 | HG002compoundhet | hetalt | 83.4699 | 71.8317 | 99.6086 | 36.1235 | 5855 | 2296 | 5853 | 23 | 22 | 95.6522 | |
| gduggal-snapplat | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 83.4678 | 77.0663 | 91.0292 | 80.6522 | 13539 | 4029 | 13577 | 1338 | 103 | 7.6981 | |
| jpowers-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 83.4657 | 81.8519 | 85.1445 | 71.6183 | 4190 | 929 | 4184 | 730 | 709 | 97.1233 | |
| gduggal-bwaplat | INDEL | * | map_l100_m2_e1 | het | 83.4646 | 72.3858 | 98.5474 | 93.4041 | 1696 | 647 | 1696 | 25 | 8 | 32.0000 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 83.4646 | 98.7578 | 72.2727 | 36.0465 | 159 | 2 | 159 | 61 | 61 | 100.0000 | |
| gduggal-snapplat | INDEL | D1_5 | map_l125_m0_e0 | homalt | 83.4646 | 71.6216 | 100.0000 | 91.9283 | 106 | 42 | 126 | 0 | 0 | ||
| egarrison-hhga | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 83.4646 | 89.8305 | 77.9412 | 76.1404 | 53 | 6 | 53 | 15 | 14 | 93.3333 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 83.4646 | 98.7578 | 72.2727 | 35.4839 | 159 | 2 | 159 | 61 | 61 | 100.0000 | |
| jmaeng-gatk | SNP | tv | map_l125_m1_e0 | * | 83.4629 | 73.2830 | 96.9274 | 85.3732 | 11737 | 4279 | 11735 | 372 | 13 | 3.4946 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 83.4621 | 71.8941 | 99.4667 | 29.5113 | 353 | 138 | 373 | 2 | 2 | 100.0000 | |