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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 | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
60301-60350 / 86044 show all | |||||||||||||||
hfeng-pmm1 | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.6399 | 99.2823 | 100.0000 | 45.3947 | 415 | 3 | 415 | 0 | 0 | ||
hfeng-pmm3 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 99.9317 | 99.8636 | 100.0000 | 45.3935 | 1464 | 2 | 1464 | 0 | 0 | ||
jmaeng-gatk | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.1381 | 99.6239 | 98.6571 | 45.3917 | 11390 | 43 | 11387 | 155 | 1 | 0.6452 | |
ckim-dragen | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 73.7279 | 98.8858 | 58.7748 | 45.3888 | 355 | 4 | 355 | 249 | 247 | 99.1968 | |
mlin-fermikit | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 84.1619 | 82.2267 | 86.1905 | 45.3886 | 7777 | 1681 | 7783 | 1247 | 1228 | 98.4763 | |
cchapple-custom | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.1110 | 97.3601 | 98.8735 | 45.3846 | 35626 | 966 | 45291 | 516 | 450 | 87.2093 | |
ltrigg-rtg1 | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.1048 | 98.5238 | 99.6927 | 45.3838 | 3604 | 54 | 3568 | 11 | 2 | 18.1818 | |
raldana-dualsentieon | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 99.3054 | 99.0537 | 99.5584 | 45.3803 | 2931 | 28 | 2931 | 13 | 0 | 0.0000 | |
anovak-vg | INDEL | D6_15 | * | het | 76.4820 | 81.7202 | 71.8750 | 45.3746 | 9473 | 2119 | 11523 | 4509 | 3518 | 78.0217 | |
rpoplin-dv42 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 98.8625 | 98.1712 | 99.5636 | 45.3709 | 8213 | 153 | 8213 | 36 | 34 | 94.4444 | |
anovak-vg | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 56.6887 | 53.0607 | 60.8492 | 45.3700 | 11806 | 10444 | 12611 | 8114 | 6224 | 76.7069 | |
cchapple-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 95.1282 | 97.8892 | 92.5187 | 45.3678 | 371 | 8 | 371 | 30 | 24 | 80.0000 | |
ckim-vqsr | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.7733 | 97.4942 | 98.0540 | 45.3637 | 9221 | 237 | 9221 | 183 | 179 | 97.8142 | |
jpowers-varprowl | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 79.4844 | 92.6189 | 69.6125 | 45.3619 | 3388 | 270 | 3395 | 1482 | 1473 | 99.3927 | |
jli-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 99.7636 | 100.0000 | 99.5283 | 45.3608 | 211 | 0 | 211 | 1 | 0 | 0.0000 | |
egarrison-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 58.3543 | 41.3584 | 99.0640 | 45.3538 | 682 | 967 | 635 | 6 | 6 | 100.0000 | |
gduggal-bwavard | INDEL | D1_5 | func_cds | het | 94.9721 | 100.0000 | 90.4255 | 45.3488 | 85 | 0 | 85 | 9 | 7 | 77.7778 | |
jlack-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_51to200 | * | 96.0289 | 93.6620 | 98.5185 | 45.3441 | 133 | 9 | 133 | 2 | 2 | 100.0000 | |
qzeng-custom | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.2828 | 99.0685 | 99.4980 | 45.3418 | 4573 | 43 | 4559 | 23 | 2 | 8.6957 | |
bgallagher-sentieon | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 100.0000 | 100.0000 | 100.0000 | 45.3409 | 481 | 0 | 481 | 0 | 0 | ||
gduggal-snapplat | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 60.7128 | 46.4157 | 87.7382 | 45.3351 | 4390 | 5068 | 4236 | 592 | 317 | 53.5473 | |
jlack-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 73.8957 | 69.0940 | 79.4146 | 45.3333 | 816 | 365 | 814 | 211 | 209 | 99.0521 | |
ckim-vqsr | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.8959 | 99.7921 | 100.0000 | 45.3303 | 480 | 1 | 480 | 0 | 0 | ||
ckim-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.8013 | 97.5893 | 98.0142 | 45.3295 | 9230 | 228 | 9230 | 187 | 180 | 96.2567 | |
jpowers-varprowl | INDEL | * | * | homalt | 92.2554 | 87.3566 | 97.7363 | 45.3284 | 109346 | 15826 | 109233 | 2530 | 2235 | 88.3399 | |
gduggal-bwavard | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 90.4018 | 83.1551 | 99.0323 | 45.3263 | 311 | 63 | 307 | 3 | 3 | 100.0000 | |
eyeh-varpipe | INDEL | D16_PLUS | HG002complexvar | homalt | 44.7304 | 49.8270 | 40.5797 | 45.3249 | 144 | 145 | 140 | 205 | 205 | 100.0000 | |
ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 60.0653 | 42.9847 | 99.6711 | 45.3237 | 337 | 447 | 303 | 1 | 1 | 100.0000 | |
eyeh-varpipe | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 90.6327 | 87.6737 | 93.7984 | 45.3197 | 1451 | 204 | 1452 | 96 | 90 | 93.7500 | |
cchapple-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 97.8606 | 97.3459 | 98.3807 | 45.3197 | 4328 | 118 | 12333 | 203 | 185 | 91.1330 | |
eyeh-varpipe | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 44.0002 | 28.5292 | 96.1301 | 45.3174 | 2029 | 5083 | 2335 | 94 | 92 | 97.8723 | |
jlack-gatk | INDEL | I16_PLUS | HG002compoundhet | hetalt | 93.0151 | 87.1476 | 99.7297 | 45.3148 | 1824 | 269 | 1845 | 5 | 4 | 80.0000 | |
ckim-dragen | SNP | tv | tech_badpromoters | * | 97.1831 | 95.8333 | 98.5714 | 45.3125 | 69 | 3 | 69 | 1 | 1 | 100.0000 | |
anovak-vg | SNP | ti | tech_badpromoters | het | 83.5443 | 75.0000 | 94.2857 | 45.3125 | 33 | 11 | 33 | 2 | 2 | 100.0000 | |
gduggal-snapvard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 98.5864 | 98.0186 | 99.1607 | 45.3115 | 841 | 17 | 827 | 7 | 4 | 57.1429 | |
eyeh-varpipe | SNP | tv | HG002compoundhet | * | 97.1567 | 99.0474 | 95.3368 | 45.3099 | 8838 | 85 | 7176 | 351 | 78 | 22.2222 | |
asubramanian-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 97.7920 | 99.4303 | 96.2068 | 45.3054 | 10298 | 59 | 10906 | 430 | 320 | 74.4186 | |
qzeng-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 89.5573 | 95.0633 | 84.6541 | 45.2951 | 3678 | 191 | 10586 | 1919 | 912 | 47.5248 | |
ndellapenna-hhga | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 94.0508 | 90.1716 | 98.2788 | 45.2919 | 578 | 63 | 571 | 10 | 10 | 100.0000 | |
anovak-vg | INDEL | I6_15 | HG002complexvar | * | 48.0486 | 41.4858 | 57.0779 | 45.2877 | 1988 | 2804 | 2008 | 1510 | 1270 | 84.1060 | |
gduggal-bwafb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 92.3938 | 89.4378 | 95.5519 | 45.2869 | 12329 | 1456 | 13383 | 623 | 612 | 98.2343 | |
ckim-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 100.0000 | 100.0000 | 100.0000 | 45.2787 | 481 | 0 | 481 | 0 | 0 | ||
anovak-vg | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 39.2875 | 29.5634 | 58.5440 | 45.2777 | 1571 | 3743 | 3080 | 2181 | 1823 | 83.5855 | |
anovak-vg | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 71.3041 | 72.8754 | 69.7991 | 45.2762 | 8095 | 3013 | 10629 | 4599 | 3296 | 71.6678 | |
astatham-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.8931 | 97.7585 | 98.0280 | 45.2710 | 9246 | 212 | 9246 | 186 | 181 | 97.3118 | |
qzeng-custom | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 86.4441 | 98.6928 | 76.9001 | 45.2692 | 151 | 2 | 1032 | 310 | 290 | 93.5484 | |
eyeh-varpipe | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 67.7028 | 91.6754 | 53.6688 | 45.2639 | 10528 | 956 | 14570 | 12578 | 12360 | 98.2668 | |
cchapple-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.9358 | 97.0774 | 98.8095 | 45.2536 | 31057 | 935 | 41417 | 499 | 447 | 89.5792 | |
mlin-fermikit | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 81.8304 | 69.7614 | 98.9490 | 45.2532 | 1871 | 811 | 1883 | 20 | 20 | 100.0000 | |
qzeng-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 89.7127 | 90.8139 | 88.6378 | 45.2529 | 10064 | 1018 | 10984 | 1408 | 719 | 51.0653 |