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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
39501-39550 / 86044 show all | |||||||||||||||
| gduggal-snapvard | SNP | * | map_l100_m2_e1 | het | 93.3754 | 96.7973 | 90.1872 | 78.6618 | 45396 | 1502 | 44805 | 4875 | 376 | 7.7128 | |
| ckim-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.6764 | 99.6119 | 99.7409 | 78.6563 | 770 | 3 | 770 | 2 | 0 | 0.0000 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.6764 | 99.6119 | 99.7409 | 78.6563 | 770 | 3 | 770 | 2 | 0 | 0.0000 | |
| ghariani-varprowl | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 17.0622 | 9.6110 | 75.9259 | 78.6561 | 42 | 395 | 41 | 13 | 13 | 100.0000 | |
| jpowers-varprowl | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 17.0622 | 9.6110 | 75.9259 | 78.6561 | 42 | 395 | 41 | 13 | 13 | 100.0000 | |
| gduggal-snapvard | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 87.6921 | 93.8506 | 82.2921 | 78.6557 | 9096 | 596 | 8997 | 1936 | 140 | 7.2314 | |
| gduggal-snapplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 56.9333 | 42.2920 | 87.0801 | 78.6542 | 310 | 423 | 337 | 50 | 17 | 34.0000 | |
| ckim-gatk | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 97.2012 | 96.5257 | 97.8862 | 78.6532 | 639 | 23 | 602 | 13 | 7 | 53.8462 | |
| jmaeng-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | hetalt | 97.4359 | 95.0000 | 100.0000 | 78.6517 | 57 | 3 | 57 | 0 | 0 | ||
| ltrigg-rtg2 | INDEL | * | map_l100_m2_e0 | homalt | 98.6382 | 97.6209 | 99.6769 | 78.6515 | 1231 | 30 | 1234 | 4 | 2 | 50.0000 | |
| bgallagher-sentieon | SNP | * | map_l150_m1_e0 | het | 98.7760 | 99.2493 | 98.3073 | 78.6499 | 19171 | 145 | 19165 | 330 | 49 | 14.8485 | |
| ltrigg-rtg1 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 98.8845 | 99.1738 | 98.5968 | 78.6472 | 6602 | 55 | 6605 | 94 | 1 | 1.0638 | |
| ciseli-custom | INDEL | I6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 56.5463 | 51.0204 | 63.4146 | 78.6458 | 25 | 24 | 26 | 15 | 14 | 93.3333 | |
| gduggal-snapfb | SNP | ti | map_l150_m1_e0 | homalt | 97.0877 | 94.6363 | 99.6694 | 78.6440 | 6934 | 393 | 6935 | 23 | 14 | 60.8696 | |
| ltrigg-rtg1 | INDEL | C6_15 | HG002complexvar | het | 99.4186 | 100.0000 | 98.8439 | 78.6420 | 4 | 0 | 171 | 2 | 0 | 0.0000 | |
| ghariani-varprowl | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 85.1516 | 96.8750 | 75.9593 | 78.6419 | 961 | 31 | 970 | 307 | 3 | 0.9772 | |
| astatham-gatk | SNP | ti | map_l150_m1_e0 | * | 91.3534 | 84.2837 | 99.7178 | 78.6410 | 16614 | 3098 | 16610 | 47 | 26 | 55.3191 | |
| jli-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 97.7503 | 97.5332 | 97.9684 | 78.6403 | 514 | 13 | 434 | 9 | 9 | 100.0000 | |
| gduggal-snapvard | SNP | * | map_l100_m2_e0 | het | 93.3360 | 96.7693 | 90.1379 | 78.6381 | 44900 | 1499 | 44319 | 4849 | 371 | 7.6511 | |
| ckim-vqsr | INDEL | I1_5 | map_siren | homalt | 99.5465 | 99.5050 | 99.5881 | 78.6343 | 1206 | 6 | 1209 | 5 | 3 | 60.0000 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 3.5874 | 1.8349 | 80.0000 | 78.6325 | 16 | 856 | 20 | 5 | 4 | 80.0000 | |
| ciseli-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 28.0702 | 17.9775 | 64.0000 | 78.6325 | 16 | 73 | 16 | 9 | 8 | 88.8889 | |
| ckim-isaac | INDEL | I1_5 | map_l125_m1_e0 | homalt | 76.5478 | 62.3853 | 99.0291 | 78.6307 | 204 | 123 | 204 | 2 | 0 | 0.0000 | |
| jpowers-varprowl | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 96.4576 | 97.6253 | 95.3175 | 78.6292 | 1480 | 36 | 1486 | 73 | 21 | 28.7671 | |
| astatham-gatk | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 97.0444 | 96.2236 | 97.8793 | 78.6262 | 637 | 25 | 600 | 13 | 8 | 61.5385 | |
| ndellapenna-hhga | SNP | ti | map_l100_m2_e1 | hetalt | 91.5254 | 87.0968 | 96.4286 | 78.6260 | 27 | 4 | 27 | 1 | 1 | 100.0000 | |
| gduggal-snapfb | SNP | tv | map_l100_m0_e0 | homalt | 97.1883 | 95.2678 | 99.1879 | 78.6252 | 3664 | 182 | 3664 | 30 | 6 | 20.0000 | |
| jlack-gatk | INDEL | I1_5 | map_siren | homalt | 99.3823 | 99.4224 | 99.3421 | 78.6217 | 1205 | 7 | 1208 | 8 | 5 | 62.5000 | |
| cchapple-custom | SNP | * | map_l125_m2_e0 | het | 96.1245 | 97.3395 | 94.9395 | 78.6207 | 28538 | 780 | 28573 | 1523 | 346 | 22.7183 | |
| jmaeng-gatk | SNP | ti | map_l100_m2_e0 | * | 89.9408 | 82.7455 | 98.5068 | 78.6206 | 40513 | 8448 | 40506 | 614 | 64 | 10.4235 | |
| ckim-gatk | INDEL | I1_5 | map_siren | homalt | 99.5056 | 99.5050 | 99.5062 | 78.6204 | 1206 | 6 | 1209 | 6 | 4 | 66.6667 | |
| anovak-vg | SNP | ti | map_l150_m1_e0 | * | 79.4593 | 85.7346 | 74.0400 | 78.6204 | 16900 | 2812 | 16756 | 5875 | 1329 | 22.6213 | |
| rpoplin-dv42 | INDEL | * | * | * | 98.9802 | 98.7882 | 99.1728 | 78.6199 | 340367 | 4175 | 340370 | 2839 | 2640 | 92.9905 | |
| ckim-dragen | SNP | * | map_l125_m2_e1 | het | 97.7443 | 98.9710 | 96.5476 | 78.6185 | 29335 | 305 | 29336 | 1049 | 91 | 8.6749 | |
| ltrigg-rtg1 | SNP | tv | map_l250_m2_e0 | het | 96.4634 | 93.5052 | 99.6150 | 78.6168 | 1814 | 126 | 1811 | 7 | 2 | 28.5714 | |
| eyeh-varpipe | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 9.9949 | 5.3085 | 85.2941 | 78.6164 | 37 | 660 | 58 | 10 | 9 | 90.0000 | |
| hfeng-pmm2 | INDEL | * | HG002compoundhet | het | 86.3875 | 82.5598 | 90.5872 | 78.6150 | 3380 | 714 | 3147 | 327 | 317 | 96.9419 | |
| gduggal-snapvard | INDEL | I6_15 | map_siren | * | 59.5493 | 55.7377 | 63.9205 | 78.6148 | 170 | 135 | 225 | 127 | 95 | 74.8031 | |
| jpowers-varprowl | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 33.2379 | 24.7453 | 50.6061 | 78.6131 | 170 | 517 | 167 | 163 | 160 | 98.1595 | |
| hfeng-pmm2 | SNP | ti | map_l125_m0_e0 | het | 98.8238 | 99.1529 | 98.4969 | 78.6095 | 8193 | 70 | 8191 | 125 | 11 | 8.8000 | |
| gduggal-snapfb | INDEL | I6_15 | map_l100_m2_e0 | * | 81.0925 | 72.4138 | 92.1348 | 78.6058 | 84 | 32 | 82 | 7 | 6 | 85.7143 | |
| gduggal-bwafb | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 94.6420 | 95.6229 | 93.6811 | 78.6041 | 18722 | 857 | 18784 | 1267 | 139 | 10.9708 | |
| gduggal-bwafb | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 94.6420 | 95.6229 | 93.6811 | 78.6041 | 18722 | 857 | 18784 | 1267 | 139 | 10.9708 | |
| mlin-fermikit | INDEL | I1_5 | map_l125_m1_e0 | het | 63.4349 | 47.1193 | 97.0339 | 78.6038 | 229 | 257 | 229 | 7 | 4 | 57.1429 | |
| egarrison-hhga | INDEL | D6_15 | map_siren | hetalt | 72.8695 | 58.5859 | 96.3636 | 78.5992 | 58 | 41 | 53 | 2 | 1 | 50.0000 | |
| qzeng-custom | SNP | tv | map_l100_m2_e0 | * | 88.2470 | 80.1862 | 98.1096 | 78.5989 | 20073 | 4960 | 20033 | 386 | 305 | 79.0155 | |
| bgallagher-sentieon | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.2107 | 98.8095 | 97.6190 | 78.5987 | 166 | 2 | 164 | 4 | 1 | 25.0000 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 83.2380 | 80.8271 | 85.7971 | 78.5980 | 215 | 51 | 296 | 49 | 48 | 97.9592 | |
| eyeh-varpipe | INDEL | D1_5 | map_siren | het | 98.6360 | 98.8142 | 98.4583 | 78.5963 | 2250 | 27 | 2363 | 37 | 14 | 37.8378 | |
| jmaeng-gatk | SNP | ti | map_l100_m2_e1 | * | 90.0240 | 82.8837 | 98.5106 | 78.5961 | 41015 | 8470 | 41008 | 620 | 64 | 10.3226 | |