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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
80251-80300 / 86044 show all | |||||||||||||||
| anovak-vg | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 37.6387 | 31.0491 | 47.7790 | 58.0455 | 367 | 815 | 441 | 482 | 356 | 73.8589 | |
| gduggal-bwafb | SNP | ti | HG002complexvar | het | 99.7807 | 99.7408 | 99.8207 | 18.4948 | 313950 | 816 | 314019 | 564 | 202 | 35.8156 | |
| gduggal-bwaplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 66.9905 | 53.7415 | 88.9096 | 95.4327 | 948 | 816 | 954 | 119 | 18 | 15.1261 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 95.2407 | 94.4809 | 96.0129 | 51.7704 | 13969 | 816 | 13967 | 580 | 530 | 91.3793 | |
| gduggal-snapfb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 92.9003 | 95.1929 | 90.7155 | 79.9240 | 16159 | 816 | 16190 | 1657 | 193 | 11.6476 | |
| gduggal-snapfb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 92.9003 | 95.1929 | 90.7155 | 79.9240 | 16159 | 816 | 16190 | 1657 | 193 | 11.6476 | |
| gduggal-snapplat | SNP | * | map_l250_m2_e1 | het | 87.7421 | 84.4985 | 91.2446 | 94.9087 | 4448 | 816 | 4450 | 427 | 204 | 47.7752 | |
| gduggal-snapvard | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 41.1383 | 38.1818 | 44.5910 | 44.9927 | 504 | 816 | 845 | 1050 | 781 | 74.3810 | |
| jpowers-varprowl | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 47.5294 | 38.2286 | 62.8109 | 62.6047 | 505 | 816 | 505 | 299 | 296 | 98.9967 | |
| ckim-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.2317 | 97.7700 | 98.6978 | 52.2722 | 35776 | 816 | 35699 | 471 | 434 | 92.1444 | |
| cchapple-custom | SNP | ti | * | homalt | 99.9468 | 99.8984 | 99.9953 | 15.1867 | 802222 | 816 | 801552 | 38 | 34 | 89.4737 | |
| ciseli-custom | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 76.2662 | 86.5448 | 68.1700 | 55.3642 | 5255 | 817 | 5230 | 2442 | 2103 | 86.1179 | |
| astatham-gatk | INDEL | D1_5 | * | * | 99.5682 | 99.4433 | 99.6934 | 60.4898 | 145928 | 817 | 145983 | 449 | 317 | 70.6013 | |
| dgrover-gatk | SNP | * | * | het | 99.9216 | 99.9564 | 99.8868 | 20.4479 | 1872770 | 817 | 1872645 | 2122 | 144 | 6.7861 | |
| egarrison-hhga | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 64.4567 | 61.1138 | 68.1865 | 74.1910 | 1284 | 817 | 1316 | 614 | 580 | 94.4625 | |
| rpoplin-dv42 | SNP | * | HG002complexvar | het | 99.8978 | 99.8245 | 99.9712 | 18.3215 | 464680 | 817 | 464534 | 134 | 101 | 75.3731 | |
| gduggal-bwaplat | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 51.2669 | 34.7444 | 97.7528 | 56.7121 | 435 | 817 | 435 | 10 | 10 | 100.0000 | |
| gduggal-snapvard | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 35.5104 | 33.6851 | 37.5449 | 56.5557 | 415 | 817 | 627 | 1043 | 747 | 71.6203 | |
| gduggal-snapplat | SNP | ti | map_l250_m2_e1 | * | 88.7551 | 83.8849 | 94.2257 | 93.7237 | 4258 | 818 | 4259 | 261 | 138 | 52.8736 | |
| gduggal-bwafb | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 96.5493 | 97.3408 | 95.7705 | 73.5567 | 29943 | 818 | 29935 | 1322 | 1296 | 98.0333 | |
| qzeng-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 91.8743 | 94.4038 | 89.4769 | 44.0923 | 13799 | 818 | 39955 | 4699 | 3029 | 64.4605 | |
| ltrigg-rtg1 | INDEL | I6_15 | HG002compoundhet | * | 94.7100 | 90.6791 | 99.1159 | 32.9210 | 7958 | 818 | 7848 | 70 | 64 | 91.4286 | |
| anovak-vg | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 77.9189 | 77.3944 | 78.4506 | 71.4753 | 2804 | 819 | 2876 | 790 | 545 | 68.9873 | |
| gduggal-snapfb | SNP | ti | map_l150_m1_e0 | * | 96.2042 | 95.8452 | 96.5660 | 76.1103 | 18893 | 819 | 18897 | 672 | 348 | 51.7857 | |
| gduggal-snapplat | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 18.7853 | 15.3926 | 24.0964 | 85.0898 | 149 | 819 | 240 | 756 | 119 | 15.7407 | |
| ckim-isaac | INDEL | I16_PLUS | * | het | 78.5832 | 69.8308 | 89.8441 | 60.3038 | 1898 | 820 | 1902 | 215 | 129 | 60.0000 | |
| egarrison-hhga | SNP | * | map_siren | * | 99.6583 | 99.4385 | 99.8791 | 53.8224 | 145407 | 821 | 145408 | 176 | 78 | 44.3182 | |
| gduggal-snapfb | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 74.5996 | 62.5114 | 92.4837 | 50.4052 | 1369 | 821 | 283 | 23 | 22 | 95.6522 | |
| anovak-vg | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 58.8731 | 57.9621 | 59.8131 | 41.7312 | 1132 | 821 | 1216 | 817 | 563 | 68.9106 | |
| gduggal-bwavard | SNP | ti | map_l100_m1_e0 | het | 95.5858 | 97.2580 | 93.9701 | 77.5354 | 29121 | 821 | 28877 | 1853 | 139 | 7.5014 | |
| gduggal-bwafb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 97.2224 | 95.1576 | 99.3788 | 72.1373 | 16153 | 822 | 16158 | 101 | 53 | 52.4752 | |
| gduggal-bwafb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 97.2224 | 95.1576 | 99.3788 | 72.1373 | 16153 | 822 | 16158 | 101 | 53 | 52.4752 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 91.9653 | 86.1570 | 98.6135 | 44.3408 | 5116 | 822 | 5121 | 72 | 60 | 83.3333 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.6832 | 96.0089 | 99.4168 | 42.4933 | 19774 | 822 | 19775 | 116 | 110 | 94.8276 | |
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.7194 | 96.0089 | 99.4918 | 41.3653 | 19774 | 822 | 19775 | 101 | 87 | 86.1386 | |
| gduggal-snapplat | SNP | tv | map_l100_m1_e0 | homalt | 95.2001 | 90.9101 | 99.9149 | 63.7649 | 8221 | 822 | 8222 | 7 | 2 | 28.5714 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 40.4600 | 27.3210 | 77.9449 | 70.7692 | 309 | 822 | 311 | 88 | 69 | 78.4091 | |
| gduggal-snapfb | SNP | ti | map_l150_m2_e0 | * | 96.3262 | 95.9877 | 96.6670 | 77.7511 | 19689 | 823 | 19693 | 679 | 349 | 51.3991 | |
| anovak-vg | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 50.7904 | 39.6185 | 70.7374 | 39.8375 | 540 | 823 | 5132 | 2123 | 1902 | 89.5902 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 60.8995 | 44.8091 | 95.0199 | 66.3989 | 669 | 824 | 954 | 50 | 47 | 94.0000 | |
| gduggal-snapfb | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 0.0000 | 0.0000 | 0.0000 | 0 | 824 | 0 | 0 | 0 | |||
| gduggal-snapplat | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 0.0000 | 0.0000 | 0.0000 | 0 | 824 | 0 | 0 | 0 | |||
| gduggal-snapplat | SNP | tv | map_l100_m2_e0 | homalt | 95.2754 | 91.0462 | 99.9166 | 66.1343 | 8389 | 825 | 8390 | 7 | 2 | 28.5714 | |
| gduggal-snapvard | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 91.8181 | 97.0493 | 87.1220 | 66.7143 | 27134 | 825 | 26966 | 3986 | 179 | 4.4907 | |
| astatham-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 96.7892 | 94.1206 | 99.6136 | 34.1069 | 13207 | 825 | 13406 | 52 | 51 | 98.0769 | |
| asubramanian-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 96.7294 | 94.6488 | 98.9035 | 60.3171 | 14592 | 825 | 15424 | 171 | 158 | 92.3977 | |
| jpowers-varprowl | SNP | * | map_l150_m2_e0 | het | 96.1913 | 95.9023 | 96.4821 | 82.5326 | 19308 | 825 | 19308 | 704 | 206 | 29.2614 | |
| gduggal-snapfb | SNP | ti | map_l100_m0_e0 | * | 96.4920 | 96.2060 | 96.7797 | 70.0719 | 20945 | 826 | 20947 | 697 | 344 | 49.3544 | |
| gduggal-snapfb | SNP | ti | map_l150_m2_e1 | * | 96.3445 | 96.0141 | 96.6772 | 77.8313 | 19897 | 826 | 19901 | 684 | 351 | 51.3158 | |
| ndellapenna-hhga | SNP | tv | HG002complexvar | het | 99.7024 | 99.4520 | 99.9540 | 21.1664 | 149905 | 826 | 149923 | 69 | 30 | 43.4783 | |