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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
76801-76850 / 86044 show all | |||||||||||||||
| ckim-gatk | SNP | * | map_l125_m2_e1 | * | 84.7700 | 74.7850 | 97.8324 | 85.1204 | 35300 | 11902 | 35294 | 782 | 60 | 7.6726 | |
| ckim-gatk | SNP | ti | map_l100_m1_e0 | het | 92.7314 | 88.0536 | 97.9342 | 80.4366 | 26365 | 3577 | 26358 | 556 | 60 | 10.7914 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 88.4335 | 83.8126 | 93.5937 | 65.9030 | 1807 | 349 | 1797 | 123 | 60 | 48.7805 | |
| cchapple-custom | INDEL | I6_15 | HG002complexvar | * | 97.5496 | 96.4942 | 98.6284 | 54.8042 | 4624 | 168 | 4746 | 66 | 60 | 90.9091 | |
| cchapple-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.8701 | 99.3283 | 98.4162 | 75.2675 | 45395 | 307 | 45425 | 731 | 60 | 8.2079 | |
| cchapple-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.8701 | 99.3283 | 98.4162 | 75.2675 | 45395 | 307 | 45425 | 731 | 60 | 8.2079 | |
| cchapple-custom | SNP | ti | HG002compoundhet | het | 99.0513 | 98.8217 | 99.2820 | 39.9079 | 9393 | 112 | 10233 | 74 | 60 | 81.0811 | |
| ciseli-custom | INDEL | * | map_l150_m0_e0 | * | 63.1351 | 56.8093 | 71.0462 | 94.9719 | 292 | 222 | 292 | 119 | 60 | 50.4202 | |
| cchapple-custom | INDEL | D1_5 | HG002complexvar | het | 99.3604 | 99.0657 | 99.6568 | 53.2015 | 20571 | 194 | 21196 | 73 | 60 | 82.1918 | |
| ciseli-custom | INDEL | D6_15 | map_l100_m1_e0 | * | 53.8462 | 51.5504 | 56.3559 | 88.4200 | 133 | 125 | 133 | 103 | 60 | 58.2524 | |
| ciseli-custom | INDEL | D6_15 | map_l100_m2_e0 | * | 54.3651 | 51.8939 | 57.0833 | 88.8786 | 137 | 127 | 137 | 103 | 60 | 58.2524 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 61.8907 | 65.6250 | 58.5586 | 70.8916 | 189 | 99 | 195 | 138 | 60 | 43.4783 | |
| ghariani-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 22.1517 | 13.2826 | 66.6667 | 82.1918 | 157 | 1025 | 156 | 78 | 60 | 76.9231 | |
| ghariani-varprowl | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | het | 61.8785 | 91.8033 | 46.6667 | 69.3095 | 56 | 5 | 56 | 64 | 60 | 93.7500 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.4090 | 99.1601 | 99.6591 | 54.8028 | 25146 | 213 | 25144 | 86 | 60 | 69.7674 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 78.0254 | 68.0540 | 91.4205 | 35.5394 | 4840 | 2272 | 650 | 61 | 60 | 98.3607 | |
| ghariani-varprowl | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | het | 76.1553 | 85.1190 | 68.8995 | 75.1486 | 143 | 25 | 144 | 65 | 61 | 93.8462 | |
| ghariani-varprowl | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 98.6127 | 99.7743 | 97.4780 | 44.0701 | 3978 | 9 | 3981 | 103 | 61 | 59.2233 | |
| hfeng-pmm1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 95.7723 | 96.7851 | 94.7804 | 58.3362 | 1144 | 38 | 1144 | 63 | 61 | 96.8254 | |
| gduggal-snapfb | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 52.4956 | 98.0106 | 35.8482 | 76.1642 | 2956 | 60 | 3022 | 5408 | 61 | 1.1280 | |
| gduggal-snapfb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 65.8825 | 97.2660 | 49.8107 | 91.6259 | 925 | 26 | 921 | 928 | 61 | 6.5733 | |
| ghariani-varprowl | INDEL | * | map_l100_m0_e0 | het | 89.7886 | 97.7473 | 83.0283 | 91.0144 | 998 | 23 | 998 | 204 | 61 | 29.9020 | |
| ghariani-varprowl | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | * | 50.5051 | 47.7707 | 53.5714 | 69.8925 | 75 | 82 | 75 | 65 | 61 | 93.8462 | |
| ghariani-varprowl | INDEL | D1_5 | segdup | het | 92.8475 | 99.4220 | 87.0886 | 96.1448 | 688 | 4 | 688 | 102 | 61 | 59.8039 | |
| gduggal-snapvard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 55.2770 | 84.4907 | 41.0749 | 86.9620 | 1095 | 201 | 1070 | 1535 | 61 | 3.9739 | |
| gduggal-snapvard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 76.8434 | 94.7617 | 64.6239 | 86.6785 | 4016 | 222 | 3986 | 2182 | 61 | 2.7956 | |
| gduggal-snapvard | SNP | ti | map_l250_m1_e0 | het | 81.6091 | 95.8895 | 71.0309 | 92.1854 | 2846 | 122 | 2832 | 1155 | 61 | 5.2814 | |
| gduggal-snapvard | INDEL | C6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 55.2980 | 100.0000 | 38.2151 | 88.1796 | 1 | 0 | 167 | 270 | 61 | 22.5926 | |
| gduggal-snapvard | INDEL | C6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 0.0000 | 0.0000 | 32.2896 | 88.3995 | 0 | 0 | 165 | 346 | 61 | 17.6301 | |
| gduggal-snapvard | INDEL | C6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 0.0000 | 0.0000 | 32.2896 | 88.3995 | 0 | 0 | 165 | 346 | 61 | 17.6301 | |
| gduggal-bwafb | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 51.9110 | 37.2480 | 85.6132 | 63.2900 | 425 | 716 | 363 | 61 | 61 | 100.0000 | |
| gduggal-bwavard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 85.8503 | 89.1304 | 82.8031 | 86.0652 | 984 | 120 | 963 | 200 | 61 | 30.5000 | |
| gduggal-bwaplat | SNP | ti | map_l100_m1_e0 | het | 86.8689 | 77.3061 | 99.1314 | 82.6916 | 23147 | 6795 | 23169 | 203 | 61 | 30.0493 | |
| eyeh-varpipe | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 23.6905 | 15.0376 | 55.7971 | 50.3597 | 20 | 113 | 77 | 61 | 61 | 100.0000 | |
| jpowers-varprowl | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | * | 49.3151 | 45.8599 | 53.3333 | 66.3342 | 72 | 85 | 72 | 63 | 61 | 96.8254 | |
| jpowers-varprowl | INDEL | D1_5 | map_l100_m1_e0 | het | 94.3765 | 95.7816 | 93.0120 | 85.5736 | 1158 | 51 | 1158 | 87 | 61 | 70.1149 | |
| jpowers-varprowl | INDEL | D1_5 | map_l100_m2_e0 | het | 94.5055 | 95.8599 | 93.1889 | 86.1907 | 1204 | 52 | 1204 | 88 | 61 | 69.3182 | |
| jpowers-varprowl | INDEL | D1_5 | segdup | het | 93.5461 | 97.3988 | 89.9866 | 95.0659 | 674 | 18 | 674 | 75 | 61 | 81.3333 | |
| jmaeng-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 92.6206 | 97.5940 | 88.1295 | 86.9820 | 649 | 16 | 490 | 66 | 61 | 92.4242 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 96.8607 | 94.4535 | 99.3939 | 46.6406 | 9894 | 581 | 10167 | 62 | 61 | 98.3871 | |
| jli-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.4310 | 96.6068 | 98.2694 | 64.7012 | 3929 | 138 | 3918 | 69 | 61 | 88.4058 | |
| rpoplin-dv42 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 92.7788 | 88.1157 | 97.9631 | 52.0232 | 3077 | 415 | 3078 | 64 | 61 | 95.3125 | |
| rpoplin-dv42 | SNP | * | HG002compoundhet | * | 99.6493 | 99.5895 | 99.7091 | 40.7188 | 25716 | 106 | 25707 | 75 | 61 | 81.3333 | |
| rpoplin-dv42 | SNP | tv | map_l150_m1_e0 | * | 98.9126 | 98.7903 | 99.0352 | 73.1204 | 10780 | 132 | 10778 | 105 | 61 | 58.0952 | |
| rpoplin-dv42 | SNP | tv | map_l150_m2_e0 | * | 98.9506 | 98.8287 | 99.0728 | 74.8529 | 11222 | 133 | 11220 | 105 | 61 | 58.0952 | |
| rpoplin-dv42 | SNP | tv | map_l150_m2_e1 | * | 98.9641 | 98.8437 | 99.0847 | 74.8658 | 11369 | 133 | 11367 | 105 | 61 | 58.0952 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 88.3297 | 92.5249 | 84.4985 | 51.0052 | 557 | 45 | 556 | 102 | 61 | 59.8039 | |
| qzeng-custom | INDEL | I1_5 | HG002complexvar | homalt | 99.1245 | 98.9887 | 99.2607 | 46.5706 | 13312 | 136 | 13292 | 99 | 61 | 61.6162 | |
| qzeng-custom | SNP | tv | map_l100_m2_e0 | homalt | 87.6918 | 78.6086 | 99.1482 | 62.9624 | 7243 | 1971 | 7217 | 62 | 61 | 98.3871 | |
| ndellapenna-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 94.6238 | 92.9702 | 96.3373 | 84.5241 | 2526 | 191 | 2525 | 96 | 61 | 63.5417 | |