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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 | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
61701-61750 / 86044 show all | |||||||||||||||
astatham-gatk | INDEL | D1_5 | func_cds | * | 100.0000 | 100.0000 | 100.0000 | 40.7407 | 159 | 0 | 160 | 0 | 0 | ||
astatham-gatk | INDEL | I6_15 | func_cds | homalt | 96.7742 | 100.0000 | 93.7500 | 40.7407 | 15 | 0 | 15 | 1 | 1 | 100.0000 | |
jli-custom | INDEL | I6_15 | func_cds | homalt | 96.7742 | 100.0000 | 93.7500 | 40.7407 | 15 | 0 | 15 | 1 | 1 | 100.0000 | |
hfeng-pmm1 | SNP | tv | tech_badpromoters | het | 98.4615 | 96.9697 | 100.0000 | 40.7407 | 32 | 1 | 32 | 0 | 0 | ||
jlack-gatk | INDEL | I6_15 | func_cds | homalt | 96.7742 | 100.0000 | 93.7500 | 40.7407 | 15 | 0 | 15 | 1 | 1 | 100.0000 | |
ckim-vqsr | INDEL | I6_15 | func_cds | homalt | 96.7742 | 100.0000 | 93.7500 | 40.7407 | 15 | 0 | 15 | 1 | 1 | 100.0000 | |
dgrover-gatk | INDEL | I6_15 | func_cds | homalt | 96.7742 | 100.0000 | 93.7500 | 40.7407 | 15 | 0 | 15 | 1 | 1 | 100.0000 | |
jlack-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 98.0972 | 99.7896 | 96.4613 | 40.7376 | 4743 | 10 | 4743 | 174 | 174 | 100.0000 | |
asubramanian-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 95.8883 | 93.1278 | 98.8175 | 40.7349 | 15557 | 1148 | 16463 | 197 | 178 | 90.3553 | |
asubramanian-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 95.8883 | 93.1278 | 98.8175 | 40.7349 | 15557 | 1148 | 16463 | 197 | 178 | 90.3553 | |
ltrigg-rtg2 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 94.9720 | 92.0000 | 98.1424 | 40.7339 | 322 | 28 | 317 | 6 | 6 | 100.0000 | |
gduggal-bwafb | INDEL | I6_15 | HG002compoundhet | hetalt | 82.7582 | 72.8242 | 95.8306 | 40.7336 | 6217 | 2320 | 1471 | 64 | 63 | 98.4375 | |
gduggal-bwafb | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.1968 | 99.5561 | 98.8400 | 40.7302 | 2467 | 11 | 2471 | 29 | 6 | 20.6897 | |
egarrison-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 82.1732 | 97.9957 | 70.7498 | 40.7293 | 7236 | 148 | 7624 | 3152 | 3088 | 97.9695 | |
anovak-vg | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 59.8171 | 57.4468 | 62.3913 | 40.7216 | 108 | 80 | 287 | 173 | 145 | 83.8150 | |
dgrover-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 95.4946 | 92.1026 | 99.1461 | 40.7199 | 898 | 77 | 1045 | 9 | 9 | 100.0000 | |
gduggal-snapvard | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 68.0107 | 68.2833 | 67.7403 | 40.7190 | 3914 | 1818 | 10936 | 5208 | 4870 | 93.5100 | |
rpoplin-dv42 | SNP | * | HG002compoundhet | * | 99.6493 | 99.5895 | 99.7091 | 40.7188 | 25716 | 106 | 25707 | 75 | 61 | 81.3333 | |
mlin-fermikit | SNP | ti | tech_badpromoters | * | 94.0476 | 92.9412 | 95.1807 | 40.7143 | 79 | 6 | 79 | 4 | 4 | 100.0000 | |
gduggal-bwafb | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 92.7348 | 88.8325 | 96.9957 | 40.7125 | 1050 | 132 | 226 | 7 | 7 | 100.0000 | |
qzeng-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 93.0202 | 94.4334 | 91.6486 | 40.7109 | 8991 | 530 | 11863 | 1081 | 1022 | 94.5421 | |
hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 94.5197 | 89.8462 | 99.7062 | 40.7085 | 876 | 99 | 1018 | 3 | 3 | 100.0000 | |
jpowers-varprowl | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.2455 | 99.2320 | 99.2591 | 40.7060 | 3876 | 30 | 3885 | 29 | 10 | 34.4828 | |
dgrover-gatk | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.3002 | 99.9010 | 98.7065 | 40.6968 | 18165 | 18 | 18162 | 238 | 4 | 1.6807 | |
ckim-isaac | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 82.4914 | 70.8428 | 98.7245 | 40.6959 | 311 | 128 | 387 | 5 | 4 | 80.0000 | |
ckim-vqsr | SNP | * | HG002complexvar | hetalt | 96.6667 | 93.5484 | 100.0000 | 40.6953 | 290 | 20 | 290 | 0 | 0 | ||
ckim-vqsr | SNP | tv | HG002complexvar | hetalt | 96.6667 | 93.5484 | 100.0000 | 40.6953 | 290 | 20 | 290 | 0 | 0 | ||
eyeh-varpipe | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 76.3850 | 99.7475 | 61.8895 | 40.6948 | 4741 | 12 | 4828 | 2973 | 2967 | 99.7982 | |
hfeng-pmm3 | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 94.2919 | 89.4359 | 99.7056 | 40.6868 | 872 | 103 | 1016 | 3 | 3 | 100.0000 | |
gduggal-snapvard | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 48.9137 | 52.6535 | 45.6699 | 40.6819 | 506 | 455 | 1176 | 1399 | 1152 | 82.3445 | |
ciseli-custom | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_51to200 | * | 50.4202 | 43.4783 | 60.0000 | 40.6780 | 20 | 26 | 21 | 14 | 13 | 92.8571 | |
eyeh-varpipe | INDEL | I16_PLUS | HG002compoundhet | hetalt | 18.8882 | 10.4634 | 96.9432 | 40.6736 | 219 | 1874 | 222 | 7 | 7 | 100.0000 | |
astatham-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.0710 | 94.4664 | 99.8233 | 40.6709 | 1673 | 98 | 1695 | 3 | 3 | 100.0000 | |
ckim-isaac | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 80.7906 | 68.5669 | 98.3181 | 40.6653 | 2622 | 1202 | 2806 | 48 | 41 | 85.4167 | |
eyeh-varpipe | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 24.7859 | 22.4655 | 27.6409 | 40.6626 | 472 | 1629 | 505 | 1322 | 1216 | 91.9818 | |
egarrison-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.2212 | 95.8530 | 98.6289 | 40.6591 | 5686 | 246 | 5683 | 79 | 58 | 73.4177 | |
ckim-vqsr | SNP | ti | HG002compoundhet | het | 99.2006 | 98.5692 | 99.8402 | 40.6564 | 9369 | 136 | 9369 | 15 | 13 | 86.6667 | |
ndellapenna-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 96.7691 | 94.9258 | 98.6854 | 40.6471 | 5631 | 301 | 5630 | 75 | 56 | 74.6667 | |
asubramanian-gatk | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 92.1790 | 86.6893 | 98.4109 | 40.6421 | 3315 | 509 | 3530 | 57 | 49 | 85.9649 | |
bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 94.6546 | 90.5641 | 99.1321 | 40.6411 | 883 | 92 | 1028 | 9 | 9 | 100.0000 | |
jpowers-varprowl | INDEL | * | func_cds | * | 91.7808 | 90.3371 | 93.2715 | 40.6336 | 402 | 43 | 402 | 29 | 28 | 96.5517 | |
hfeng-pmm1 | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.6310 | 99.3377 | 99.9260 | 40.6323 | 4050 | 27 | 4053 | 3 | 0 | 0.0000 | |
astatham-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 95.3282 | 91.7949 | 99.1445 | 40.6321 | 895 | 80 | 1043 | 9 | 9 | 100.0000 | |
ckim-isaac | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 89.9396 | 84.3248 | 96.3555 | 40.6305 | 5826 | 1083 | 5843 | 221 | 166 | 75.1131 | |
jlack-gatk | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.2883 | 99.8050 | 98.7768 | 40.6294 | 4607 | 9 | 4603 | 57 | 3 | 5.2632 | |
anovak-vg | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_51to200 | het | 44.5986 | 69.2308 | 32.8947 | 40.6250 | 9 | 4 | 25 | 51 | 46 | 90.1961 | |
gduggal-bwafb | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 75.8133 | 61.0478 | 100.0000 | 40.6250 | 268 | 171 | 19 | 0 | 0 | ||
gduggal-bwafb | INDEL | D1_5 | tech_badpromoters | * | 100.0000 | 100.0000 | 100.0000 | 40.6250 | 19 | 0 | 19 | 0 | 0 | ||
eyeh-varpipe | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 79.6904 | 73.7069 | 86.7312 | 40.6237 | 342 | 122 | 1255 | 192 | 190 | 98.9583 | |
jlack-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 92.0250 | 86.0513 | 98.8900 | 40.6231 | 839 | 136 | 980 | 11 | 10 | 90.9091 |