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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
7701-7750 / 86044 show all | |||||||||||||||
| egarrison-hhga | INDEL | * | * | hetalt | 84.7197 | 74.1293 | 98.8404 | 62.3270 | 18708 | 6529 | 18156 | 213 | 191 | 89.6714 | |
| ckim-isaac | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 83.9473 | 78.4628 | 90.2562 | 82.3482 | 1858 | 510 | 1973 | 213 | 125 | 58.6854 | |
| ckim-vqsr | SNP | * | map_l150_m2_e0 | het | 78.1444 | 64.8041 | 98.4007 | 91.6936 | 13047 | 7086 | 13044 | 212 | 2 | 0.9434 | |
| eyeh-varpipe | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 50.9371 | 34.6330 | 96.2465 | 52.9921 | 3846 | 7259 | 5436 | 212 | 205 | 96.6981 | |
| egarrison-hhga | INDEL | D16_PLUS | HG002compoundhet | het | 73.4421 | 80.9877 | 67.1827 | 49.1339 | 328 | 77 | 434 | 212 | 201 | 94.8113 | |
| gduggal-snapvard | INDEL | C1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 0.0000 | 0.0000 | 9.4017 | 83.5211 | 0 | 0 | 22 | 212 | 16 | 7.5472 | |
| ghariani-varprowl | INDEL | D1_5 | map_l100_m1_e0 | het | 91.4439 | 99.0074 | 84.9539 | 88.4423 | 1197 | 12 | 1197 | 212 | 63 | 29.7170 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 74.0703 | 72.3684 | 75.8542 | 64.2217 | 660 | 252 | 666 | 212 | 139 | 65.5660 | |
| anovak-vg | INDEL | D1_5 | map_l125_m2_e1 | het | 82.1373 | 88.5714 | 76.5746 | 87.9814 | 682 | 88 | 693 | 212 | 70 | 33.0189 | |
| astatham-gatk | INDEL | D6_15 | * | het | 98.7915 | 99.4048 | 98.1857 | 62.8008 | 11523 | 69 | 11473 | 212 | 175 | 82.5472 | |
| jmaeng-gatk | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.6504 | 99.6818 | 99.6191 | 61.4842 | 55454 | 177 | 55443 | 212 | 23 | 10.8491 | |
| jpowers-varprowl | SNP | tv | map_l150_m0_e0 | * | 95.1094 | 95.2803 | 94.9391 | 85.9113 | 3977 | 197 | 3977 | 212 | 55 | 25.9434 | |
| hfeng-pmm2 | SNP | * | map_l125_m0_e0 | het | 98.6818 | 99.0287 | 98.3373 | 78.8543 | 12541 | 123 | 12538 | 212 | 20 | 9.4340 | |
| 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-bwafb | INDEL | I1_5 | HG002compoundhet | het | 91.6005 | 86.8235 | 96.9338 | 46.2155 | 738 | 112 | 6702 | 212 | 180 | 84.9057 | |
| ndellapenna-hhga | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.3149 | 99.0149 | 99.6167 | 57.6636 | 55083 | 548 | 55098 | 212 | 134 | 63.2075 | |
| qzeng-custom | INDEL | I16_PLUS | HG002compoundhet | homalt | 5.3812 | 100.0000 | 2.7650 | 59.0566 | 3 | 0 | 6 | 211 | 173 | 81.9905 | |
| rpoplin-dv42 | SNP | * | * | homalt | 99.9769 | 99.9716 | 99.9821 | 18.2100 | 1179826 | 335 | 1179802 | 211 | 157 | 74.4076 | |
| cchapple-custom | INDEL | I6_15 | HG002compoundhet | homalt | 19.1571 | 100.0000 | 10.5932 | 65.6477 | 31 | 0 | 25 | 211 | 211 | 100.0000 | |
| ciseli-custom | INDEL | C1_5 | HG002compoundhet | homalt | 0.0000 | 0.0000 | 5.3812 | 85.0736 | 0 | 0 | 12 | 211 | 81 | 38.3886 | |
| gduggal-snapplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 89.0414 | 87.1669 | 90.9983 | 69.2267 | 2126 | 313 | 2133 | 211 | 14 | 6.6351 | |
| gduggal-snapfb | SNP | tv | map_l150_m0_e0 | het | 94.5988 | 96.4122 | 92.8523 | 78.6628 | 2741 | 102 | 2741 | 211 | 84 | 39.8104 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 86.8145 | 81.4642 | 92.9171 | 53.5981 | 2615 | 595 | 2768 | 211 | 211 | 100.0000 | |
| gduggal-bwaplat | SNP | ti | map_l100_m2_e1 | het | 87.2661 | 77.9360 | 99.1339 | 83.6711 | 24129 | 6831 | 24151 | 211 | 63 | 29.8578 | |
| gduggal-bwavard | INDEL | * | map_l150_m1_e0 | * | 90.3416 | 95.3662 | 85.8199 | 91.3779 | 1276 | 62 | 1277 | 211 | 47 | 22.2749 | |
| ltrigg-rtg1 | INDEL | * | * | homalt | 99.6060 | 99.3824 | 99.8305 | 54.1259 | 124398 | 773 | 124268 | 211 | 185 | 87.6777 | |
| jmaeng-gatk | SNP | * | HG002complexvar | het | 99.7155 | 99.4778 | 99.9544 | 19.1665 | 463066 | 2431 | 462938 | 211 | 65 | 30.8057 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 90.3150 | 97.0389 | 84.4624 | 59.0100 | 1147 | 35 | 1147 | 211 | 208 | 98.5782 | |
| jlack-gatk | INDEL | * | segdup | * | 95.2733 | 98.4742 | 92.2739 | 95.5954 | 2517 | 39 | 2520 | 211 | 15 | 7.1090 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 73.8957 | 69.0940 | 79.4146 | 45.3333 | 816 | 365 | 814 | 211 | 209 | 99.0521 | |
| hfeng-pmm1 | INDEL | I6_15 | * | homalt | 98.1442 | 99.5993 | 96.7310 | 48.9389 | 6214 | 25 | 6214 | 210 | 209 | 99.5238 | |
| jlack-gatk | INDEL | I6_15 | * | het | 97.9846 | 98.0664 | 97.9029 | 60.0128 | 9839 | 194 | 9804 | 210 | 112 | 53.3333 | |
| cchapple-custom | SNP | tv | HG002complexvar | het | 99.7615 | 99.6630 | 99.8602 | 21.5432 | 150223 | 508 | 149954 | 210 | 146 | 69.5238 | |
| cchapple-custom | SNP | tv | map_l150_m0_e0 | * | 95.4922 | 95.9751 | 95.0142 | 82.7299 | 4006 | 168 | 4002 | 210 | 43 | 20.4762 | |
| cchapple-custom | SNP | tv | map_l150_m0_e0 | het | 94.6151 | 96.4122 | 92.8838 | 85.0097 | 2741 | 102 | 2741 | 210 | 43 | 20.4762 | |
| qzeng-custom | INDEL | D16_PLUS | map_l100_m1_e0 | * | 36.3200 | 81.6092 | 23.3577 | 88.6542 | 71 | 16 | 64 | 210 | 1 | 0.4762 | |
| mlin-fermikit | INDEL | * | map_l125_m2_e1 | * | 69.4080 | 58.1573 | 86.0558 | 82.7274 | 1294 | 931 | 1296 | 210 | 161 | 76.6667 | |
| ndellapenna-hhga | INDEL | I6_15 | * | het | 97.5570 | 97.2192 | 97.8973 | 54.2636 | 9754 | 279 | 9777 | 210 | 127 | 60.4762 | |
| ndellapenna-hhga | SNP | * | HG002compoundhet | homalt | 98.7381 | 99.4064 | 98.0787 | 35.7852 | 10718 | 64 | 10720 | 210 | 197 | 93.8095 | |
| ckim-isaac | INDEL | D16_PLUS | HG002compoundhet | het | 48.4816 | 76.0494 | 35.5828 | 39.9632 | 308 | 97 | 116 | 210 | 182 | 86.6667 | |
| egarrison-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 99.0697 | 98.8184 | 99.3222 | 69.4679 | 30775 | 368 | 30774 | 210 | 73 | 34.7619 | |
| egarrison-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 99.0697 | 98.8184 | 99.3222 | 69.4679 | 30775 | 368 | 30774 | 210 | 73 | 34.7619 | |
| bgallagher-sentieon | SNP | tv | map_l100_m1_e0 | het | 99.1089 | 99.5719 | 98.6501 | 70.0769 | 15351 | 66 | 15347 | 210 | 25 | 11.9048 | |
| asubramanian-gatk | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.0957 | 98.9522 | 99.2395 | 65.0592 | 27388 | 290 | 27403 | 210 | 22 | 10.4762 | |
| rpoplin-dv42 | SNP | ti | map_siren | * | 99.6562 | 99.5227 | 99.7902 | 53.3616 | 99876 | 479 | 99868 | 210 | 138 | 65.7143 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.6195 | 96.5975 | 98.6634 | 57.7294 | 15501 | 546 | 15502 | 210 | 201 | 95.7143 | |
| raldana-dualsentieon | INDEL | I1_5 | * | het | 99.5073 | 99.2827 | 99.7331 | 57.9285 | 78474 | 567 | 78457 | 210 | 142 | 67.6190 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.2425 | 97.6560 | 98.8360 | 46.5565 | 17831 | 428 | 17832 | 210 | 208 | 99.0476 | |
| gduggal-snapfb | SNP | ti | segdup | het | 98.8224 | 99.3766 | 98.2744 | 91.5559 | 11955 | 75 | 11960 | 210 | 13 | 6.1905 | |
| gduggal-snapvard | INDEL | I6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 47.5592 | 44.5161 | 51.0490 | 71.9424 | 69 | 86 | 219 | 210 | 175 | 83.3333 | |