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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
951-1000 / 86044 show all | |||||||||||||||
| ckim-isaac | SNP | * | map_l150_m1_e0 | het | 73.7957 | 58.6094 | 99.6041 | 78.9632 | 11321 | 7995 | 11322 | 45 | 8 | 17.7778 | |
| mlin-fermikit | SNP | * | map_l150_m0_e0 | * | 47.5288 | 33.5688 | 81.3658 | 64.0159 | 4039 | 7993 | 4039 | 925 | 818 | 88.4324 | |
| asubramanian-gatk | SNP | tv | map_l100_m0_e0 | * | 43.7760 | 28.0314 | 99.8714 | 92.3134 | 3107 | 7977 | 3107 | 4 | 1 | 25.0000 | |
| qzeng-custom | SNP | * | * | homalt | 99.6134 | 99.3243 | 99.9041 | 17.3884 | 1172188 | 7974 | 1162090 | 1115 | 707 | 63.4081 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 59.0651 | 56.3393 | 62.0679 | 49.1269 | 10287 | 7972 | 10307 | 6299 | 4780 | 75.8851 | |
| ckim-vqsr | SNP | tv | map_siren | homalt | 69.9947 | 53.8399 | 100.0000 | 68.1997 | 9282 | 7958 | 9279 | 0 | 0 | ||
| gduggal-bwaplat | SNP | ti | map_siren | het | 92.8447 | 87.2527 | 99.2026 | 72.7353 | 54430 | 7952 | 54492 | 438 | 111 | 25.3425 | |
| ciseli-custom | SNP | tv | HG002complexvar | * | 94.9824 | 96.7736 | 93.2564 | 24.4003 | 238213 | 7942 | 236085 | 17072 | 2875 | 16.8404 | |
| ndellapenna-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 88.6086 | 87.8487 | 89.3817 | 86.9060 | 57410 | 7941 | 58141 | 6907 | 5920 | 85.7101 | |
| ndellapenna-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 88.6086 | 87.8487 | 89.3817 | 86.9060 | 57410 | 7941 | 58141 | 6907 | 5920 | 85.7101 | |
| mlin-fermikit | SNP | ti | map_l125_m0_e0 | * | 52.3097 | 37.7919 | 84.9392 | 57.8951 | 4823 | 7939 | 4822 | 855 | 764 | 89.3567 | |
| mlin-fermikit | SNP | ti | map_l150_m2_e1 | het | 56.1207 | 39.2931 | 98.1570 | 69.2394 | 5114 | 7901 | 5113 | 96 | 5 | 5.2083 | |
| ckim-isaac | INDEL | * | * | het | 96.5214 | 95.9358 | 97.1142 | 48.5384 | 186243 | 7890 | 184953 | 5496 | 3918 | 71.2882 | |
| gduggal-snapplat | SNP | ti | HG002complexvar | het | 97.6877 | 97.4934 | 97.8828 | 21.8010 | 306876 | 7890 | 307493 | 6651 | 990 | 14.8850 | |
| egarrison-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 88.6605 | 87.9344 | 89.3987 | 86.9048 | 57466 | 7885 | 57984 | 6876 | 6009 | 87.3909 | |
| egarrison-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 88.6605 | 87.9344 | 89.3987 | 86.9048 | 57466 | 7885 | 57984 | 6876 | 6009 | 87.3909 | |
| gduggal-bwaplat | SNP | tv | map_l100_m2_e1 | * | 81.3480 | 68.8368 | 99.4174 | 84.4949 | 17404 | 7879 | 17405 | 102 | 20 | 19.6078 | |
| qzeng-custom | SNP | ti | HG002complexvar | * | 99.1315 | 98.4529 | 99.8194 | 18.2769 | 500571 | 7866 | 493623 | 893 | 400 | 44.7928 | |
| gduggal-bwaplat | SNP | tv | map_l100_m2_e0 | * | 81.2147 | 68.6414 | 99.4272 | 84.5184 | 17183 | 7850 | 17184 | 99 | 19 | 19.1919 | |
| mlin-fermikit | SNP | ti | map_l150_m2_e0 | het | 55.8942 | 39.0731 | 98.1471 | 68.9855 | 5033 | 7848 | 5032 | 95 | 5 | 5.2632 | |
| ciseli-custom | INDEL | D6_15 | * | hetalt | 0.0000 | 4.0372 | 0.0000 | 0.0000 | 330 | 7844 | 0 | 0 | 0 | ||
| gduggal-bwaplat | SNP | tv | map_l100_m1_e0 | * | 80.7967 | 68.0462 | 99.4275 | 83.4681 | 16672 | 7829 | 16673 | 96 | 19 | 19.7917 | |
| astatham-gatk | SNP | ti | HG002complexvar | * | 99.2181 | 98.4614 | 99.9866 | 17.7102 | 500613 | 7823 | 500548 | 67 | 41 | 61.1940 | |
| ciseli-custom | INDEL | D6_15 | HG002compoundhet | hetalt | 0.0000 | 4.0486 | 0.0000 | 0.0000 | 330 | 7821 | 0 | 0 | 0 | ||
| ckim-isaac | SNP | * | map_l100_m0_e0 | het | 77.3393 | 63.1643 | 99.7172 | 71.7888 | 13394 | 7811 | 13397 | 38 | 6 | 15.7895 | |
| gduggal-snapplat | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 29.4305 | 22.6149 | 42.1263 | 81.2487 | 2278 | 7795 | 2734 | 3756 | 1082 | 28.8072 | |
| qzeng-custom | SNP | * | HG002complexvar | het | 99.0563 | 98.3261 | 99.7975 | 19.7489 | 457708 | 7792 | 449025 | 911 | 250 | 27.4424 | |
| ckim-vqsr | SNP | ti | map_l125_m2_e1 | homalt | 48.4929 | 32.0126 | 99.9455 | 86.0864 | 3668 | 7790 | 3668 | 2 | 2 | 100.0000 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 61.8393 | 51.5519 | 77.2561 | 71.5347 | 8288 | 7789 | 8261 | 2432 | 2302 | 94.6546 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 61.8393 | 51.5519 | 77.2561 | 71.5347 | 8288 | 7789 | 8261 | 2432 | 2302 | 94.6546 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 0.0000 | 4.7473 | 0.0000 | 0.0000 | 388 | 7785 | 0 | 0 | 0 | ||
| gduggal-snapfb | INDEL | I6_15 | * | * | 76.3979 | 68.7024 | 86.0349 | 35.3787 | 17054 | 7769 | 17786 | 2887 | 2798 | 96.9172 | |
| jpowers-varprowl | INDEL | * | HG002complexvar | * | 91.1605 | 89.9127 | 92.4435 | 54.5762 | 69177 | 7761 | 68949 | 5636 | 5349 | 94.9077 | |
| ckim-vqsr | SNP | ti | map_l125_m2_e0 | homalt | 48.2602 | 31.8102 | 99.9447 | 86.1579 | 3613 | 7745 | 3613 | 2 | 2 | 100.0000 | |
| ciseli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 0.0000 | 4.0700 | 0.0000 | 0.0000 | 328 | 7731 | 0 | 0 | 0 | ||
| ciseli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 0.0000 | 4.0700 | 0.0000 | 0.0000 | 328 | 7731 | 0 | 0 | 0 | ||
| ciseli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 0.0000 | 4.6943 | 0.0000 | 0.0000 | 380 | 7715 | 0 | 0 | 0 | ||
| mlin-fermikit | SNP | ti | map_l150_m1_e0 | het | 54.4721 | 37.6880 | 98.2090 | 64.1838 | 4662 | 7708 | 4661 | 85 | 5 | 5.8824 | |
| anovak-vg | INDEL | I1_5 | * | hetalt | 0.0000 | 31.2282 | 0.0000 | 0.0000 | 3496 | 7699 | 0 | 0 | 0 | ||
| gduggal-snapplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 64.2360 | 57.8454 | 72.2140 | 63.0306 | 10562 | 7697 | 13647 | 5251 | 3074 | 58.5412 | |
| eyeh-varpipe | INDEL | D1_5 | * | * | 95.6258 | 94.7617 | 96.5059 | 56.5047 | 139058 | 7687 | 139038 | 5034 | 4747 | 94.2988 | |
| anovak-vg | INDEL | I1_5 | HG002compoundhet | hetalt | 0.0000 | 31.2338 | 0.0000 | 0.0000 | 3491 | 7686 | 0 | 0 | 0 | ||
| gduggal-snapplat | INDEL | D6_15 | * | het | 45.6195 | 33.7388 | 70.4153 | 67.7429 | 3911 | 7681 | 3018 | 1268 | 180 | 14.1956 | |
| ckim-isaac | INDEL | I1_5 | * | * | 96.6542 | 94.9085 | 98.4652 | 49.5628 | 142993 | 7671 | 142942 | 2228 | 1638 | 73.5189 | |
| astatham-gatk | SNP | ti | HG002complexvar | het | 98.7599 | 97.5636 | 99.9860 | 17.3084 | 307097 | 7669 | 307042 | 43 | 17 | 39.5349 | |
| ckim-vqsr | SNP | ti | map_l125_m1_e0 | homalt | 46.9945 | 30.7198 | 99.9411 | 85.1863 | 3393 | 7652 | 3393 | 2 | 2 | 100.0000 | |
| anovak-vg | SNP | * | map_siren | het | 84.8820 | 91.5981 | 79.0836 | 63.1144 | 83346 | 7645 | 82394 | 21792 | 4974 | 22.8249 | |
| gduggal-bwavard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 61.8858 | 52.4538 | 75.4536 | 73.3552 | 8433 | 7644 | 8318 | 2706 | 2382 | 88.0266 | |
| gduggal-bwavard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 61.8858 | 52.4538 | 75.4536 | 73.3552 | 8433 | 7644 | 8318 | 2706 | 2382 | 88.0266 | |
| ckim-vqsr | SNP | tv | map_l125_m2_e1 | * | 69.8938 | 54.1334 | 98.6002 | 89.6003 | 9017 | 7640 | 9016 | 128 | 1 | 0.7813 | |