PrecisionFDA
Truth Challenge
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Explore HG002 comparison results
Use this interactive explorer to filter all results across submission entries and multiple dimensions.
| Entry | Type | Subtype | Subset | Genotype | F-score | Recall | Precision | Frac_NA | Truth TP | Truth FN | Query TP | Query FP | FP gt | % FP ma | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
73501-73550 / 86044 show all | |||||||||||||||
| ckim-isaac | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 84.3015 | 79.4055 | 89.8409 | 68.3211 | 748 | 194 | 734 | 83 | 52 | 62.6506 | |
| ckim-vqsr | SNP | ti | HG002compoundhet | homalt | 98.6436 | 97.3763 | 99.9445 | 31.0556 | 7200 | 194 | 7200 | 4 | 4 | 100.0000 | |
| gduggal-bwafb | SNP | tv | HG002complexvar | homalt | 99.8685 | 99.7960 | 99.9410 | 22.9952 | 94917 | 194 | 94931 | 56 | 49 | 87.5000 | |
| gduggal-bwaplat | INDEL | * | map_l250_m2_e0 | * | 58.5470 | 41.3897 | 100.0000 | 98.8731 | 137 | 194 | 137 | 0 | 0 | ||
| gduggal-bwaplat | INDEL | * | map_l250_m2_e1 | * | 58.8983 | 41.7417 | 100.0000 | 98.8871 | 139 | 194 | 139 | 0 | 0 | ||
| gduggal-bwaplat | INDEL | D1_5 | map_l150_m1_e0 | het | 74.4186 | 59.7510 | 98.6301 | 96.0087 | 288 | 194 | 288 | 4 | 1 | 25.0000 | |
| gduggal-bwavard | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 2.9557 | 1.5228 | 50.0000 | 87.7551 | 3 | 194 | 3 | 3 | 2 | 66.6667 | |
| eyeh-varpipe | SNP | * | map_l100_m2_e0 | * | 98.6905 | 99.7377 | 97.6651 | 69.5065 | 73770 | 194 | 71526 | 1710 | 51 | 2.9825 | |
| eyeh-varpipe | SNP | * | map_l100_m2_e1 | * | 98.6948 | 99.7404 | 97.6710 | 69.5344 | 74543 | 194 | 72256 | 1723 | 51 | 2.9600 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 63.1380 | 46.2604 | 99.4048 | 57.0332 | 167 | 194 | 167 | 1 | 1 | 100.0000 | |
| ndellapenna-hhga | SNP | tv | map_l150_m1_e0 | * | 98.9384 | 98.2221 | 99.6652 | 71.6791 | 10718 | 194 | 10718 | 36 | 17 | 47.2222 | |
| qzeng-custom | INDEL | * | map_l125_m1_e0 | homalt | 83.3361 | 73.4973 | 96.2162 | 85.8482 | 538 | 194 | 712 | 28 | 10 | 35.7143 | |
| ltrigg-rtg2 | SNP | tv | * | homalt | 99.9678 | 99.9486 | 99.9870 | 19.3650 | 376927 | 194 | 376951 | 49 | 41 | 83.6735 | |
| ndellapenna-hhga | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 87.3110 | 82.9974 | 92.0976 | 77.0179 | 947 | 194 | 944 | 81 | 55 | 67.9012 | |
| anovak-vg | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 96.9087 | 96.8629 | 96.9546 | 55.9921 | 5990 | 194 | 6049 | 190 | 95 | 50.0000 | |
| asubramanian-gatk | INDEL | * | map_l150_m1_e0 | * | 89.9819 | 85.5007 | 94.9587 | 97.6598 | 1144 | 194 | 1149 | 61 | 7 | 11.4754 | |
| asubramanian-gatk | INDEL | D1_5 | map_l100_m1_e0 | * | 92.8980 | 89.5022 | 96.5618 | 87.1490 | 1654 | 194 | 1657 | 59 | 7 | 11.8644 | |
| hfeng-pmm1 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 98.4463 | 97.0858 | 99.8455 | 77.6924 | 6463 | 194 | 6463 | 10 | 0 | 0.0000 | |
| hfeng-pmm2 | SNP | * | map_l150_m1_e0 | * | 99.2283 | 99.3662 | 99.0908 | 76.3631 | 30415 | 194 | 30409 | 279 | 34 | 12.1864 | |
| jlack-gatk | INDEL | I6_15 | * | het | 97.9846 | 98.0664 | 97.9029 | 60.0128 | 9839 | 194 | 9804 | 210 | 112 | 53.3333 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 93.0016 | 90.9261 | 95.1741 | 68.8082 | 1944 | 194 | 1913 | 97 | 35 | 36.0825 | |
| cchapple-custom | INDEL | D1_5 | HG002complexvar | het | 99.3604 | 99.0657 | 99.6568 | 53.2015 | 20571 | 194 | 21196 | 73 | 60 | 82.1918 | |
| ciseli-custom | INDEL | D6_15 | map_siren | * | 62.3762 | 61.8861 | 62.8743 | 84.5131 | 315 | 194 | 315 | 186 | 97 | 52.1505 | |
| jli-custom | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.7287 | 96.3493 | 99.1483 | 61.3786 | 5120 | 194 | 5122 | 44 | 31 | 70.4545 | |
| jpowers-varprowl | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 97.9586 | 98.9331 | 97.0031 | 50.6413 | 17989 | 194 | 18029 | 557 | 149 | 26.7504 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 39.6010 | 27.0677 | 73.7500 | 90.5101 | 72 | 194 | 59 | 21 | 4 | 19.0476 | |
| gduggal-snapvard | INDEL | * | map_l100_m2_e1 | homalt | 91.1844 | 84.8556 | 98.5333 | 76.7370 | 1087 | 194 | 1478 | 22 | 18 | 81.8182 | |
| gduggal-snapplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 66.9912 | 56.0811 | 83.1715 | 93.2356 | 249 | 195 | 257 | 52 | 22 | 42.3077 | |
| jlack-gatk | SNP | * | map_l150_m2_e1 | homalt | 99.0927 | 98.3512 | 99.8455 | 71.6669 | 11632 | 195 | 11632 | 18 | 13 | 72.2222 | |
| hfeng-pmm2 | SNP | * | map_l150_m2_e0 | * | 99.2475 | 99.3878 | 99.1076 | 77.7218 | 31657 | 195 | 31651 | 285 | 34 | 11.9298 | |
| hfeng-pmm2 | SNP | * | map_l150_m2_e1 | * | 99.2528 | 99.3946 | 99.1113 | 77.7651 | 32015 | 195 | 32009 | 287 | 34 | 11.8467 | |
| hfeng-pmm3 | SNP | * | map_l125_m1_e0 | het | 99.4129 | 99.3132 | 99.5129 | 70.9946 | 28197 | 195 | 28191 | 138 | 13 | 9.4203 | |
| ndellapenna-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 97.8924 | 97.1669 | 98.6287 | 80.6797 | 6688 | 195 | 6689 | 93 | 28 | 30.1075 | |
| qzeng-custom | INDEL | I1_5 | map_l150_m2_e0 | * | 76.0546 | 62.4277 | 97.2917 | 93.6809 | 324 | 195 | 467 | 13 | 8 | 61.5385 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 84.0119 | 76.3636 | 93.3628 | 58.1998 | 630 | 195 | 633 | 45 | 38 | 84.4444 | |
| ckim-isaac | INDEL | I16_PLUS | HG002complexvar | homalt | 50.1099 | 36.8932 | 78.0822 | 66.5138 | 114 | 195 | 114 | 32 | 13 | 40.6250 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 84.0119 | 76.3636 | 93.3628 | 58.1998 | 630 | 195 | 633 | 45 | 38 | 84.4444 | |
| gduggal-bwavard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 81.2556 | 88.9456 | 74.7895 | 89.6153 | 1569 | 195 | 1510 | 509 | 141 | 27.7014 | |
| gduggal-bwavard | SNP | ti | map_l150_m2_e0 | homalt | 98.6236 | 97.4396 | 99.8368 | 73.2710 | 7421 | 195 | 7339 | 12 | 9 | 75.0000 | |
| gduggal-snapfb | INDEL | * | map_l100_m2_e0 | het | 93.1137 | 91.5475 | 94.7345 | 82.7714 | 2112 | 195 | 2159 | 120 | 22 | 18.3333 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 57.0752 | 40.9091 | 94.3662 | 86.2934 | 135 | 195 | 134 | 8 | 3 | 37.5000 | |
| anovak-vg | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 80.3562 | 86.2869 | 75.1884 | 83.1152 | 1227 | 195 | 1397 | 461 | 231 | 50.1085 | |
| astatham-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.4954 | 95.1601 | 99.9482 | 25.7593 | 3834 | 195 | 3860 | 2 | 2 | 100.0000 | |
| asubramanian-gatk | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.3035 | 98.8131 | 99.7988 | 59.4317 | 16234 | 195 | 16370 | 33 | 3 | 9.0909 | |
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.7097 | 96.3304 | 99.1289 | 64.0826 | 5119 | 195 | 5121 | 45 | 38 | 84.4444 | |
| ltrigg-rtg1 | SNP | ti | map_l250_m2_e0 | het | 96.8039 | 94.0074 | 99.7719 | 81.1683 | 3059 | 195 | 3062 | 7 | 2 | 28.5714 | |
| ltrigg-rtg1 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 97.7725 | 95.8037 | 99.8239 | 42.4645 | 4452 | 195 | 4535 | 8 | 8 | 100.0000 | |
| rpoplin-dv42 | SNP | ti | map_l125_m2_e0 | het | 99.1665 | 98.9669 | 99.3669 | 71.7774 | 18681 | 195 | 18677 | 119 | 74 | 62.1849 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 95.1163 | 94.9599 | 95.2731 | 65.4635 | 3674 | 195 | 3628 | 180 | 177 | 98.3333 | |
| raldana-dualsentieon | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 95.4371 | 91.9154 | 99.2394 | 60.4914 | 2217 | 195 | 2218 | 17 | 11 | 64.7059 | |