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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
73301-73350 / 86044 show all | |||||||||||||||
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 93.8776 | 89.9023 | 98.2206 | 65.9944 | 1656 | 186 | 1656 | 30 | 21 | 70.0000 | |
| jli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.6957 | 98.3216 | 99.0726 | 47.6211 | 10896 | 186 | 10896 | 102 | 98 | 96.0784 | |
| jpowers-varprowl | INDEL | * | map_l125_m2_e0 | * | 93.0771 | 91.5301 | 94.6773 | 88.3364 | 2010 | 186 | 2010 | 113 | 79 | 69.9115 | |
| dgrover-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.6126 | 95.3835 | 99.9483 | 25.9281 | 3843 | 186 | 3869 | 2 | 2 | 100.0000 | |
| gduggal-bwavard | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 98.2001 | 97.4711 | 98.9400 | 41.0943 | 7169 | 186 | 7094 | 76 | 20 | 26.3158 | |
| gduggal-bwavard | SNP | * | map_l150_m0_e0 | het | 89.4308 | 97.6574 | 82.4825 | 88.0388 | 7754 | 186 | 7675 | 1630 | 60 | 3.6810 | |
| gduggal-bwaplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 72.8837 | 58.1081 | 97.7358 | 91.6876 | 258 | 186 | 259 | 6 | 5 | 83.3333 | |
| astatham-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 97.2350 | 94.7249 | 99.8818 | 43.0518 | 3340 | 186 | 3381 | 4 | 4 | 100.0000 | |
| astatham-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 97.2350 | 94.7249 | 99.8818 | 43.0518 | 3340 | 186 | 3381 | 4 | 4 | 100.0000 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 97.9986 | 97.0872 | 98.9273 | 73.5231 | 6233 | 187 | 7378 | 80 | 61 | 76.2500 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 97.9986 | 97.0872 | 98.9273 | 73.5231 | 6233 | 187 | 7378 | 80 | 61 | 76.2500 | |
| astatham-gatk | SNP | * | map_l100_m1_e0 | homalt | 99.6081 | 99.3075 | 99.9106 | 57.8259 | 26816 | 187 | 26816 | 24 | 19 | 79.1667 | |
| anovak-vg | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 63.8608 | 71.3629 | 57.7860 | 51.0477 | 466 | 187 | 783 | 572 | 499 | 87.2378 | |
| astatham-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.2925 | 98.9506 | 97.6432 | 71.0801 | 17632 | 187 | 17235 | 416 | 367 | 88.2212 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 81.1540 | 77.3058 | 85.4054 | 60.1508 | 637 | 187 | 632 | 108 | 59 | 54.6296 | |
| hfeng-pmm2 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 96.6345 | 95.4020 | 97.8993 | 66.6779 | 3880 | 187 | 3868 | 83 | 65 | 78.3133 | |
| hfeng-pmm3 | INDEL | I6_15 | * | het | 98.8597 | 98.1362 | 99.5939 | 56.2294 | 9846 | 187 | 9811 | 40 | 29 | 72.5000 | |
| hfeng-pmm1 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 96.1312 | 95.1667 | 97.1154 | 62.9013 | 3682 | 187 | 3636 | 108 | 104 | 96.2963 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 2.6042 | 100.0000 | 5 | 187 | 0 | 0 | 0 | ||||
| gduggal-snapplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 59.4534 | 45.9538 | 84.1837 | 88.0196 | 159 | 187 | 165 | 31 | 5 | 16.1290 | |
| cchapple-custom | SNP | tv | map_l125_m2_e0 | homalt | 98.4215 | 96.8921 | 100.0000 | 65.2969 | 5830 | 187 | 5827 | 0 | 0 | ||
| cchapple-custom | SNP | tv | map_l125_m2_e1 | homalt | 98.4366 | 96.9213 | 100.0000 | 65.3352 | 5887 | 187 | 5884 | 0 | 0 | ||
| ckim-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.3059 | 99.0585 | 99.5546 | 59.8847 | 19675 | 187 | 19668 | 88 | 46 | 52.2727 | |
| ltrigg-rtg2 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 98.5354 | 97.7762 | 99.3066 | 59.4807 | 8222 | 187 | 8306 | 58 | 19 | 32.7586 | |
| mlin-fermikit | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 92.1665 | 91.3265 | 93.0222 | 72.9912 | 1969 | 187 | 1973 | 148 | 100 | 67.5676 | |
| raldana-dualsentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 95.5177 | 91.4612 | 99.9507 | 31.0075 | 2003 | 187 | 2026 | 1 | 1 | 100.0000 | |
| gduggal-bwaplat | SNP | tv | segdup | * | 98.5186 | 97.8083 | 99.2394 | 94.9737 | 8345 | 187 | 8350 | 64 | 11 | 17.1875 | |
| gduggal-bwavard | SNP | ti | map_l150_m1_e0 | homalt | 98.6247 | 97.4478 | 99.8303 | 71.2444 | 7140 | 187 | 7059 | 12 | 9 | 75.0000 | |
| gduggal-snapfb | INDEL | * | map_l100_m1_e0 | het | 93.1246 | 91.6331 | 94.6655 | 81.5482 | 2048 | 187 | 2094 | 118 | 21 | 17.7966 | |
| egarrison-hhga | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 91.8274 | 91.5346 | 92.1220 | 61.6285 | 2022 | 187 | 2023 | 173 | 118 | 68.2081 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 76.2995 | 61.9145 | 99.3921 | 30.0000 | 304 | 187 | 327 | 2 | 2 | 100.0000 | |
| ckim-isaac | INDEL | I1_5 | map_l150_m2_e1 | * | 78.2708 | 64.7834 | 98.8506 | 91.4496 | 344 | 187 | 344 | 4 | 1 | 25.0000 | |
| egarrison-hhga | INDEL | D6_15 | HG002complexvar | het | 93.0974 | 94.0064 | 92.2058 | 56.4938 | 2933 | 187 | 2993 | 253 | 209 | 82.6087 | |
| ckim-isaac | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 94.3567 | 89.4171 | 99.8741 | 46.5320 | 1580 | 187 | 1586 | 2 | 1 | 50.0000 | |
| ckim-isaac | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 68.3908 | 54.5894 | 91.5323 | 59.3443 | 226 | 188 | 227 | 21 | 15 | 71.4286 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 91.3280 | 92.3546 | 90.3239 | 69.1828 | 2271 | 188 | 2231 | 239 | 158 | 66.1088 | |
| dgrover-gatk | SNP | tv | HG002complexvar | * | 99.9486 | 99.9236 | 99.9736 | 22.0729 | 245964 | 188 | 245873 | 65 | 32 | 49.2308 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 95.0420 | 91.4155 | 98.9681 | 33.4097 | 2002 | 188 | 2014 | 21 | 20 | 95.2381 | |
| egarrison-hhga | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.9850 | 98.7098 | 99.2618 | 74.4815 | 14383 | 188 | 14387 | 107 | 31 | 28.9720 | |
| egarrison-hhga | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.9850 | 98.7098 | 99.2618 | 74.4815 | 14383 | 188 | 14387 | 107 | 31 | 28.9720 | |
| ckim-vqsr | SNP | tv | HG002compoundhet | * | 98.8066 | 97.8931 | 99.7373 | 49.7301 | 8735 | 188 | 8732 | 23 | 15 | 65.2174 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 93.9195 | 88.9930 | 99.4234 | 30.1878 | 1520 | 188 | 1552 | 9 | 8 | 88.8889 | |
| mlin-fermikit | INDEL | * | map_l250_m1_e0 | * | 52.1158 | 38.3607 | 81.2500 | 92.0966 | 117 | 188 | 117 | 27 | 20 | 74.0741 | |
| mlin-fermikit | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 95.9832 | 96.0537 | 95.9128 | 70.7498 | 4576 | 188 | 4576 | 195 | 106 | 54.3590 | |
| mlin-fermikit | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 95.0821 | 95.4655 | 94.7017 | 82.7295 | 3958 | 188 | 3968 | 222 | 134 | 60.3604 | |
| ndellapenna-hhga | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 89.7651 | 91.4894 | 88.1046 | 61.3701 | 2021 | 188 | 2022 | 273 | 186 | 68.1319 | |
| ltrigg-rtg2 | INDEL | D1_5 | HG002complexvar | het | 99.3002 | 99.0946 | 99.5066 | 51.3766 | 20577 | 188 | 20368 | 101 | 44 | 43.5644 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 92.6020 | 89.7937 | 95.5916 | 62.8768 | 1654 | 188 | 1648 | 76 | 46 | 60.5263 | |
| gduggal-snapfb | SNP | tv | HG002compoundhet | * | 79.6649 | 97.8931 | 67.1595 | 54.5136 | 8735 | 188 | 8812 | 4309 | 247 | 5.7322 | |
| ghariani-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 77.2126 | 92.3546 | 66.3363 | 73.7008 | 2271 | 188 | 2276 | 1155 | 1093 | 94.6320 | |