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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
23951-24000 / 86044 show all | |||||||||||||||
| cchapple-custom | INDEL | I6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 98.7336 | 98.3871 | 99.0826 | 83.5347 | 61 | 1 | 108 | 1 | 0 | 0.0000 | |
| ckim-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.5392 | 100.0000 | 99.0826 | 67.8940 | 216 | 0 | 216 | 2 | 2 | 100.0000 | |
| egarrison-hhga | SNP | tv | * | hetalt | 99.1394 | 99.1963 | 99.0826 | 48.4024 | 864 | 7 | 864 | 8 | 8 | 100.0000 | |
| egarrison-hhga | SNP | * | * | hetalt | 99.1394 | 99.1963 | 99.0826 | 48.4024 | 864 | 7 | 864 | 8 | 8 | 100.0000 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.5392 | 100.0000 | 99.0826 | 68.3599 | 216 | 0 | 216 | 2 | 2 | 100.0000 | |
| ckim-vqsr | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.5392 | 100.0000 | 99.0826 | 67.8940 | 216 | 0 | 216 | 2 | 2 | 100.0000 | |
| ckim-vqsr | INDEL | I6_15 | map_l100_m1_e0 | * | 96.8610 | 94.7368 | 99.0826 | 89.8321 | 108 | 6 | 108 | 1 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | * | func_cds | het | 99.5392 | 100.0000 | 99.0826 | 50.3417 | 214 | 0 | 216 | 2 | 0 | 0.0000 | |
| ltrigg-rtg1 | INDEL | I1_5 | map_siren | hetalt | 97.2768 | 95.5357 | 99.0826 | 91.7674 | 107 | 5 | 108 | 1 | 1 | 100.0000 | |
| bgallagher-sentieon | INDEL | I1_5 | map_l100_m2_e1 | homalt | 99.5392 | 100.0000 | 99.0826 | 81.8454 | 540 | 0 | 540 | 5 | 4 | 80.0000 | |
| astatham-gatk | INDEL | * | func_cds | het | 99.5392 | 100.0000 | 99.0826 | 50.0000 | 214 | 0 | 216 | 2 | 0 | 0.0000 | |
| astatham-gatk | INDEL | I1_5 | map_l100_m2_e1 | homalt | 99.5392 | 100.0000 | 99.0826 | 82.0606 | 540 | 0 | 540 | 5 | 4 | 80.0000 | |
| bgallagher-sentieon | INDEL | * | func_cds | het | 99.5392 | 100.0000 | 99.0826 | 49.7696 | 214 | 0 | 216 | 2 | 0 | 0.0000 | |
| raldana-dualsentieon | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.5392 | 100.0000 | 99.0826 | 66.3060 | 216 | 0 | 216 | 2 | 2 | 100.0000 | |
| rpoplin-dv42 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 97.7376 | 96.4286 | 99.0826 | 75.1708 | 108 | 4 | 108 | 1 | 1 | 100.0000 | |
| hfeng-pmm1 | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.5392 | 100.0000 | 99.0826 | 64.4372 | 216 | 0 | 216 | 2 | 2 | 100.0000 | |
| hfeng-pmm2 | INDEL | I1_5 | map_l100_m2_e1 | homalt | 99.5392 | 100.0000 | 99.0826 | 80.8099 | 540 | 0 | 540 | 5 | 4 | 80.0000 | |
| hfeng-pmm2 | INDEL | I6_15 | map_l100_m2_e0 | * | 96.0000 | 93.1034 | 99.0826 | 87.7390 | 108 | 8 | 108 | 1 | 1 | 100.0000 | |
| hfeng-pmm2 | INDEL | I6_15 | map_l100_m2_e1 | * | 96.0000 | 93.1034 | 99.0826 | 87.9956 | 108 | 8 | 108 | 1 | 1 | 100.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l100_m2_e1 | homalt | 99.5392 | 100.0000 | 99.0826 | 80.4869 | 540 | 0 | 540 | 5 | 3 | 60.0000 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 74.4454 | 59.6206 | 99.0826 | 87.0083 | 220 | 149 | 216 | 2 | 1 | 50.0000 | |
| gduggal-bwafb | INDEL | D16_PLUS | HG002compoundhet | hetalt | 86.2756 | 76.4004 | 99.0826 | 35.1190 | 1473 | 455 | 216 | 2 | 2 | 100.0000 | |
| eyeh-varpipe | SNP | tv | map_l125_m2_e1 | hetalt | 99.5392 | 100.0000 | 99.0826 | 73.6715 | 30 | 0 | 108 | 1 | 0 | 0.0000 | |
| hfeng-pmm1 | INDEL | D1_5 | HG002compoundhet | * | 95.7858 | 92.7013 | 99.0826 | 62.4019 | 11342 | 893 | 11341 | 105 | 101 | 96.1905 | |
| anovak-vg | SNP | * | HG002complexvar | homalt | 98.2895 | 97.5091 | 99.0824 | 19.5966 | 281387 | 7188 | 273293 | 2531 | 2130 | 84.1565 | |
| dgrover-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.9105 | 98.7393 | 99.0822 | 76.8986 | 2428 | 31 | 2375 | 22 | 13 | 59.0909 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 91.8091 | 85.5307 | 99.0822 | 46.3398 | 2329 | 394 | 2375 | 22 | 22 | 100.0000 | |
| cchapple-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.4934 | 99.9080 | 99.0821 | 64.7126 | 2172 | 2 | 2159 | 20 | 1 | 5.0000 | |
| ltrigg-rtg2 | INDEL | * | map_l125_m2_e1 | * | 97.7940 | 96.5393 | 99.0817 | 82.5509 | 2148 | 77 | 2158 | 20 | 1 | 5.0000 | |
| gduggal-bwaplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 93.4119 | 88.3559 | 99.0817 | 66.5438 | 2155 | 284 | 2158 | 20 | 6 | 30.0000 | |
| ltrigg-rtg2 | INDEL | C1_5 | HG002complexvar | * | 91.9145 | 85.7143 | 99.0816 | 88.0866 | 6 | 1 | 971 | 9 | 3 | 33.3333 | |
| rpoplin-dv42 | INDEL | * | map_l125_m2_e0 | homalt | 99.0164 | 98.9515 | 99.0814 | 86.1076 | 755 | 8 | 755 | 7 | 6 | 85.7143 | |
| hfeng-pmm1 | INDEL | * | map_siren | het | 98.4945 | 97.9148 | 99.0811 | 80.4769 | 4414 | 94 | 4421 | 41 | 3 | 7.3171 | |
| ckim-gatk | INDEL | I1_5 | map_l100_m2_e1 | homalt | 99.4465 | 99.8148 | 99.0809 | 82.4799 | 539 | 1 | 539 | 5 | 4 | 80.0000 | |
| dgrover-gatk | INDEL | I1_5 | map_l100_m2_e1 | homalt | 99.4465 | 99.8148 | 99.0809 | 82.3434 | 539 | 1 | 539 | 5 | 4 | 80.0000 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 99.2803 | 99.4811 | 99.0803 | 50.1719 | 10353 | 54 | 10342 | 96 | 88 | 91.6667 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 99.2755 | 99.4715 | 99.0802 | 50.4204 | 10352 | 55 | 10341 | 96 | 89 | 92.7083 | |
| anovak-vg | SNP | tv | map_l150_m2_e1 | homalt | 87.3530 | 78.1084 | 99.0798 | 73.8866 | 3229 | 905 | 3230 | 30 | 23 | 76.6667 | |
| gduggal-bwavard | INDEL | I1_5 | map_l125_m2_e0 | homalt | 97.1572 | 95.3079 | 99.0798 | 78.1940 | 325 | 16 | 323 | 3 | 1 | 33.3333 | |
| cchapple-custom | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.1220 | 97.1827 | 99.0797 | 47.1607 | 15316 | 444 | 34988 | 325 | 263 | 80.9231 | |
| ckim-vqsr | SNP | ti | map_l125_m2_e0 | * | 70.8577 | 55.1491 | 99.0796 | 88.2228 | 16687 | 13571 | 16685 | 155 | 5 | 3.2258 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 98.5348 | 97.9964 | 99.0792 | 78.0340 | 538 | 11 | 538 | 5 | 4 | 80.0000 | |
| jmaeng-gatk | INDEL | I1_5 | map_l100_m2_e1 | homalt | 99.3536 | 99.6296 | 99.0792 | 82.1733 | 538 | 2 | 538 | 5 | 4 | 80.0000 | |
| astatham-gatk | INDEL | I1_5 | map_l100_m2_e0 | * | 96.5143 | 94.0789 | 99.0790 | 85.3464 | 1287 | 81 | 1291 | 12 | 4 | 33.3333 | |
| jli-custom | SNP | tv | segdup | het | 99.3872 | 99.6974 | 99.0789 | 90.9422 | 5271 | 16 | 5271 | 49 | 0 | 0.0000 | |
| jmaeng-gatk | INDEL | * | map_l125_m2_e0 | homalt | 98.8838 | 98.6894 | 99.0789 | 86.9841 | 753 | 10 | 753 | 7 | 4 | 57.1429 | |
| egarrison-hhga | INDEL | * | map_l125_m2_e0 | homalt | 98.8838 | 98.6894 | 99.0789 | 86.4407 | 753 | 10 | 753 | 7 | 4 | 57.1429 | |
| ckim-isaac | INDEL | I1_5 | map_l125_m2_e0 | homalt | 77.0609 | 63.0499 | 99.0783 | 80.6250 | 215 | 126 | 215 | 2 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l125_m2_e1 | * | 98.8490 | 98.6207 | 99.0783 | 85.5790 | 858 | 12 | 860 | 8 | 2 | 25.0000 | |
| ckim-isaac | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 96.6063 | 94.2548 | 99.0780 | 47.3389 | 2789 | 170 | 2794 | 26 | 6 | 23.0769 | |