PrecisionFDA
Truth Challenge
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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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
69901-69950 / 86044 show all | |||||||||||||||
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 98.3871 | 98.1609 | 98.6143 | 65.7437 | 427 | 8 | 427 | 6 | 1 | 16.6667 | |
| bgallagher-sentieon | INDEL | I16_PLUS | HG002complexvar | * | 98.3871 | 97.8610 | 98.9189 | 67.3392 | 1281 | 28 | 1281 | 14 | 14 | 100.0000 | |
| ndellapenna-hhga | INDEL | I1_5 | map_l125_m0_e0 | * | 98.3871 | 98.3871 | 98.3871 | 88.2620 | 305 | 5 | 305 | 5 | 1 | 20.0000 | |
| ckim-vqsr | INDEL | D16_PLUS | HG002complexvar | het | 98.3872 | 98.7353 | 98.0415 | 69.0000 | 1093 | 14 | 851 | 17 | 10 | 58.8235 | |
| gduggal-bwavard | SNP | * | map_l125_m0_e0 | homalt | 98.3897 | 97.0501 | 99.7668 | 70.8893 | 6514 | 198 | 6417 | 15 | 11 | 73.3333 | |
| rpoplin-dv42 | INDEL | I1_5 | map_l125_m0_e0 | * | 98.3897 | 98.3871 | 98.3923 | 88.1388 | 305 | 5 | 306 | 5 | 1 | 20.0000 | |
| dgrover-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.3899 | 99.7736 | 97.0441 | 62.0464 | 11458 | 26 | 11458 | 349 | 339 | 97.1347 | |
| ckim-isaac | SNP | ti | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 98.3899 | 96.9496 | 99.8736 | 43.2587 | 3941 | 124 | 3951 | 5 | 2 | 40.0000 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 98.3899 | 99.9450 | 96.8825 | 62.1062 | 3636 | 2 | 3636 | 117 | 115 | 98.2906 | |
| gduggal-snapvard | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 98.3899 | 98.2619 | 98.5182 | 61.1046 | 6897 | 122 | 6848 | 103 | 31 | 30.0971 | |
| jli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 98.3908 | 98.3908 | 98.3908 | 65.9891 | 428 | 7 | 428 | 7 | 3 | 42.8571 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 98.3908 | 98.3908 | 98.3908 | 69.9793 | 428 | 7 | 428 | 7 | 3 | 42.8571 | |
| anovak-vg | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 98.3912 | 98.6014 | 98.1818 | 44.9656 | 846 | 12 | 864 | 16 | 14 | 87.5000 | |
| gduggal-bwavard | SNP | tv | HG002complexvar | homalt | 98.3914 | 96.9047 | 99.9244 | 20.9085 | 92167 | 2944 | 89912 | 68 | 35 | 51.4706 | |
| astatham-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.3923 | 97.0109 | 99.8136 | 86.7219 | 1071 | 33 | 1071 | 2 | 2 | 100.0000 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 98.3923 | 99.2303 | 97.5682 | 62.2540 | 3610 | 28 | 3611 | 90 | 84 | 93.3333 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 98.3923 | 96.8354 | 100.0000 | 72.8559 | 306 | 10 | 307 | 0 | 0 | ||
| astatham-gatk | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.3926 | 98.2240 | 98.5619 | 60.1500 | 15762 | 285 | 15763 | 230 | 217 | 94.3478 | |
| gduggal-bwavard | SNP | tv | segdup | homalt | 98.3926 | 97.4676 | 99.3354 | 90.2442 | 3156 | 82 | 3139 | 21 | 19 | 90.4762 | |
| jli-custom | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 98.3930 | 99.3902 | 97.4155 | 59.5008 | 489 | 3 | 490 | 13 | 11 | 84.6154 | |
| asubramanian-gatk | SNP | ti | HG002compoundhet | homalt | 98.3931 | 96.8894 | 99.9442 | 30.6032 | 7164 | 230 | 7164 | 4 | 3 | 75.0000 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.3938 | 98.5294 | 98.2585 | 65.1438 | 1072 | 16 | 1072 | 19 | 14 | 73.6842 | |
| jlack-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 98.3939 | 98.9796 | 97.8151 | 89.1397 | 1746 | 18 | 1746 | 39 | 21 | 53.8462 | |
| astatham-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.3940 | 99.7649 | 97.0603 | 61.7981 | 11457 | 27 | 11457 | 347 | 341 | 98.2709 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 98.3942 | 97.3988 | 99.4100 | 77.7413 | 337 | 9 | 337 | 2 | 1 | 50.0000 | |
| ndellapenna-hhga | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.3946 | 98.1976 | 98.5925 | 80.3787 | 1471 | 27 | 1471 | 21 | 19 | 90.4762 | |
| hfeng-pmm2 | INDEL | D1_5 | map_l125_m2_e0 | * | 98.3954 | 99.1251 | 97.6764 | 86.9350 | 1133 | 10 | 1135 | 27 | 4 | 14.8148 | |
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 98.3957 | 100.0000 | 96.8421 | 69.7452 | 92 | 0 | 92 | 3 | 3 | 100.0000 | |
| raldana-dualsentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 98.3957 | 100.0000 | 96.8421 | 68.8525 | 92 | 0 | 92 | 3 | 3 | 100.0000 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.3958 | 98.0100 | 98.7847 | 73.2093 | 591 | 12 | 569 | 7 | 3 | 42.8571 | |
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.3958 | 98.0100 | 98.7847 | 72.5975 | 591 | 12 | 569 | 7 | 3 | 42.8571 | |
| mlin-fermikit | SNP | tv | segdup | homalt | 98.3960 | 98.5485 | 98.2440 | 87.6277 | 3191 | 47 | 3189 | 57 | 49 | 85.9649 | |
| astatham-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.3963 | 97.8441 | 98.9547 | 72.8220 | 590 | 13 | 568 | 6 | 2 | 33.3333 | |
| hfeng-pmm3 | SNP | tv | map_l250_m1_e0 | het | 98.3966 | 97.8735 | 98.9253 | 88.0822 | 1749 | 38 | 1749 | 19 | 0 | 0.0000 | |
| ltrigg-rtg1 | SNP | * | map_l150_m1_e0 | het | 98.3972 | 97.0957 | 99.7341 | 63.5971 | 18755 | 561 | 18755 | 50 | 9 | 18.0000 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 98.3975 | 98.7234 | 98.0737 | 43.5889 | 464 | 6 | 1782 | 35 | 13 | 37.1429 | |
| astatham-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 98.3979 | 97.1519 | 99.6764 | 72.8471 | 307 | 9 | 308 | 1 | 1 | 100.0000 | |
| dgrover-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 98.3979 | 97.1519 | 99.6764 | 72.8471 | 307 | 9 | 308 | 1 | 1 | 100.0000 | |
| jli-custom | SNP | ti | map_l250_m2_e0 | * | 98.3980 | 97.5040 | 99.3085 | 86.8596 | 4883 | 125 | 4883 | 34 | 18 | 52.9412 | |
| ltrigg-rtg2 | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 98.3982 | 97.2756 | 99.5471 | 54.5040 | 3035 | 85 | 3077 | 14 | 13 | 92.8571 | |
| bgallagher-sentieon | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 98.3982 | 97.2851 | 99.5370 | 91.0596 | 215 | 6 | 215 | 1 | 1 | 100.0000 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 98.3982 | 98.8506 | 97.9499 | 70.1564 | 430 | 5 | 430 | 9 | 4 | 44.4444 | |
| ckim-dragen | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 98.3982 | 99.5370 | 97.2851 | 67.4041 | 215 | 1 | 215 | 6 | 6 | 100.0000 | |
| rpoplin-dv42 | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.3984 | 98.6070 | 98.1907 | 77.5143 | 6017 | 85 | 6024 | 111 | 100 | 90.0901 | |
| asubramanian-gatk | INDEL | D6_15 | * | het | 98.3985 | 98.5594 | 98.2382 | 63.4201 | 11425 | 167 | 11375 | 204 | 176 | 86.2745 | |
| mlin-fermikit | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 98.3986 | 97.4766 | 99.3382 | 61.3636 | 1352 | 35 | 1351 | 9 | 1 | 11.1111 | |
| qzeng-custom | SNP | ti | segdup | het | 98.3988 | 98.8030 | 97.9978 | 93.2216 | 11886 | 144 | 11845 | 242 | 6 | 2.4793 | |
| mlin-fermikit | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 98.3991 | 99.3730 | 97.4441 | 42.0040 | 3962 | 25 | 3965 | 104 | 97 | 93.2692 | |
| ltrigg-rtg1 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.3992 | 97.1808 | 99.6485 | 64.4597 | 586 | 17 | 567 | 2 | 0 | 0.0000 | |
| ckim-dragen | SNP | * | map_l125_m1_e0 | * | 98.3997 | 99.0866 | 97.7222 | 72.8507 | 44913 | 414 | 44919 | 1047 | 117 | 11.1748 | |