PrecisionFDA
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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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
1801-1850 / 86044 show all | |||||||||||||||
| gduggal-snapfb | INDEL | I1_5 | HG002complexvar | * | 93.5109 | 94.6378 | 92.4106 | 55.4813 | 31574 | 1789 | 31902 | 2620 | 888 | 33.8931 | |
| qzeng-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 94.0704 | 96.0794 | 92.1437 | 38.7632 | 8038 | 328 | 10849 | 925 | 888 | 96.0000 | |
| gduggal-bwavard | SNP | tv | HG002complexvar | het | 98.2582 | 97.4538 | 99.0760 | 23.1907 | 146896 | 3838 | 144431 | 1347 | 888 | 65.9243 | |
| jpowers-varprowl | INDEL | * | HG002complexvar | homalt | 94.9661 | 93.9024 | 96.0543 | 47.7714 | 25379 | 1648 | 25269 | 1038 | 887 | 85.4528 | |
| hfeng-pmm1 | INDEL | * | * | * | 99.3397 | 99.0289 | 99.6526 | 57.3618 | 341196 | 3346 | 341057 | 1189 | 887 | 74.6005 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 79.7753 | 86.5705 | 73.9693 | 64.8607 | 3062 | 475 | 3032 | 1067 | 886 | 83.0366 | |
| anovak-vg | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 36.6612 | 27.4933 | 55.0021 | 33.8540 | 204 | 538 | 1281 | 1048 | 886 | 84.5420 | |
| jpowers-varprowl | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 65.5149 | 76.6385 | 57.2111 | 69.3456 | 1181 | 360 | 1198 | 896 | 886 | 98.8839 | |
| anovak-vg | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 44.0797 | 45.6816 | 42.5864 | 46.2713 | 439 | 522 | 764 | 1030 | 885 | 85.9223 | |
| mlin-fermikit | SNP | tv | map_l150_m2_e1 | * | 57.3730 | 43.7750 | 83.2258 | 66.7620 | 5035 | 6467 | 5031 | 1014 | 885 | 87.2781 | |
| mlin-fermikit | SNP | tv | map_l150_m2_e1 | homalt | 60.4772 | 53.3382 | 69.8227 | 60.3864 | 2205 | 1929 | 2205 | 953 | 885 | 92.8646 | |
| qzeng-custom | INDEL | I6_15 | HG002compoundhet | * | 75.9258 | 69.2571 | 84.0157 | 36.6439 | 6078 | 2698 | 5992 | 1140 | 884 | 77.5439 | |
| jpowers-varprowl | SNP | ti | HG002compoundhet | homalt | 92.3856 | 99.8107 | 85.9888 | 37.4563 | 7380 | 14 | 7383 | 1203 | 882 | 73.3167 | |
| eyeh-varpipe | INDEL | D16_PLUS | HG002compoundhet | * | 28.2801 | 22.7680 | 37.3134 | 28.0307 | 533 | 1808 | 525 | 882 | 881 | 99.8866 | |
| gduggal-bwaplat | SNP | ti | * | * | 99.0047 | 98.3196 | 99.6994 | 24.2468 | 2050467 | 35044 | 2050804 | 6183 | 880 | 14.2326 | |
| ghariani-varprowl | SNP | ti | HG002compoundhet | homalt | 92.9457 | 99.8242 | 86.9540 | 37.0935 | 7381 | 13 | 7385 | 1108 | 880 | 79.4224 | |
| ckim-isaac | SNP | * | * | * | 98.5357 | 97.1616 | 99.9494 | 15.9907 | 2967930 | 86704 | 2968584 | 1504 | 880 | 58.5106 | |
| gduggal-bwaplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 77.5469 | 65.0258 | 96.0400 | 78.6649 | 42495 | 22856 | 42490 | 1752 | 879 | 50.1712 | |
| gduggal-bwaplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 77.5469 | 65.0258 | 96.0400 | 78.6649 | 42495 | 22856 | 42490 | 1752 | 879 | 50.1712 | |
| gduggal-snapvard | INDEL | D6_15 | HG002complexvar | * | 66.6908 | 61.3353 | 73.0708 | 52.3301 | 3252 | 2050 | 3229 | 1190 | 878 | 73.7815 | |
| ghariani-varprowl | INDEL | D6_15 | HG002complexvar | het | 84.7743 | 95.1923 | 76.4117 | 58.8552 | 2970 | 150 | 2977 | 919 | 877 | 95.4298 | |
| hfeng-pmm2 | INDEL | * | HG002compoundhet | * | 94.6829 | 92.5968 | 96.8651 | 60.5702 | 27742 | 2218 | 27624 | 894 | 877 | 98.0984 | |
| astatham-gatk | INDEL | * | HG002compoundhet | homalt | 60.8541 | 99.7085 | 43.7900 | 84.6320 | 684 | 2 | 684 | 878 | 876 | 99.7722 | |
| jpowers-varprowl | INDEL | I6_15 | HG002complexvar | * | 68.3061 | 61.4775 | 76.8413 | 54.9585 | 2946 | 1846 | 2963 | 893 | 875 | 97.9843 | |
| ciseli-custom | SNP | tv | map_siren | homalt | 92.1923 | 91.6589 | 92.7320 | 56.2107 | 15802 | 1438 | 15770 | 1236 | 874 | 70.7120 | |
| ndellapenna-hhga | INDEL | * | HG002compoundhet | homalt | 54.9045 | 96.9388 | 38.2979 | 70.2430 | 665 | 21 | 666 | 1073 | 874 | 81.4539 | |
| jpowers-varprowl | INDEL | D6_15 | HG002complexvar | het | 82.3223 | 90.1603 | 75.7381 | 57.2412 | 2813 | 307 | 2822 | 904 | 873 | 96.5708 | |
| gduggal-snapvard | INDEL | I16_PLUS | * | * | 2.3476 | 1.2075 | 42.0851 | 50.8200 | 77 | 6300 | 1098 | 1511 | 872 | 57.7101 | |
| gduggal-bwaplat | SNP | * | HG002complexvar | het | 97.5069 | 96.6621 | 98.3666 | 21.6545 | 449959 | 15538 | 450835 | 7486 | 872 | 11.6484 | |
| qzeng-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 94.4069 | 93.3537 | 95.4842 | 40.6110 | 22909 | 1631 | 24020 | 1136 | 871 | 76.6725 | |
| ghariani-varprowl | INDEL | I6_15 | HG002complexvar | * | 71.5536 | 66.2145 | 77.8293 | 58.1077 | 3173 | 1619 | 3191 | 909 | 871 | 95.8196 | |
| gduggal-bwavard | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 31.7698 | 26.2547 | 40.2181 | 60.9567 | 633 | 1778 | 627 | 932 | 870 | 93.3476 | |
| qzeng-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 92.6354 | 91.1441 | 94.1762 | 35.9848 | 16642 | 1617 | 17303 | 1070 | 870 | 81.3084 | |
| qzeng-custom | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.6704 | 98.1255 | 97.2195 | 71.9856 | 32613 | 623 | 41783 | 1195 | 869 | 72.7197 | |
| mlin-fermikit | SNP | tv | map_l150_m2_e0 | * | 57.2030 | 43.5755 | 83.2323 | 66.6536 | 4948 | 6407 | 4944 | 996 | 869 | 87.2490 | |
| mlin-fermikit | SNP | tv | map_l150_m2_e0 | homalt | 60.3616 | 53.1472 | 69.8423 | 60.3244 | 2170 | 1913 | 2170 | 937 | 869 | 92.7428 | |
| anovak-vg | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 95.3736 | 96.4849 | 94.2876 | 62.2229 | 34174 | 1245 | 35108 | 2127 | 869 | 40.8557 | |
| ckim-gatk | INDEL | * | HG002compoundhet | homalt | 61.0169 | 99.7085 | 43.9589 | 84.7301 | 684 | 2 | 684 | 872 | 869 | 99.6560 | |
| gduggal-bwavard | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 52.1029 | 79.6221 | 38.7203 | 60.5927 | 590 | 151 | 587 | 929 | 868 | 93.4338 | |
| gduggal-bwafb | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 81.8128 | 74.8933 | 90.1411 | 58.1664 | 7544 | 2529 | 8942 | 978 | 867 | 88.6503 | |
| qzeng-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 82.4233 | 87.4656 | 77.9307 | 54.2101 | 1905 | 273 | 5378 | 1523 | 867 | 56.9271 | |
| ckim-vqsr | INDEL | * | HG002compoundhet | homalt | 61.0714 | 99.7085 | 44.0154 | 84.7468 | 684 | 2 | 684 | 870 | 867 | 99.6552 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 90.4147 | 91.9985 | 88.8845 | 55.6709 | 14763 | 1284 | 15793 | 1975 | 866 | 43.8481 | |
| gduggal-snapplat | SNP | tv | * | het | 98.3145 | 98.0664 | 98.5638 | 36.3598 | 580263 | 11441 | 580658 | 8461 | 866 | 10.2352 | |
| eyeh-varpipe | INDEL | D16_PLUS | * | homalt | 49.8532 | 50.8274 | 48.9155 | 43.2091 | 860 | 832 | 857 | 895 | 865 | 96.6480 | |
| gduggal-bwavard | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 43.1783 | 40.0414 | 46.8485 | 64.6530 | 774 | 1159 | 773 | 877 | 864 | 98.5177 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 82.4109 | 89.4163 | 76.4235 | 49.0835 | 3278 | 388 | 3248 | 1002 | 864 | 86.2275 | |
| anovak-vg | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 35.7126 | 30.6097 | 42.8571 | 50.7598 | 738 | 1673 | 861 | 1148 | 864 | 75.2613 | |
| anovak-vg | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 73.8753 | 73.0416 | 74.7283 | 69.3443 | 3739 | 1380 | 3850 | 1302 | 863 | 66.2826 | |
| ghariani-varprowl | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 72.8517 | 89.6171 | 61.3706 | 74.5275 | 1381 | 160 | 1406 | 885 | 863 | 97.5141 | |