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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
4551-4600 / 86044 show all | |||||||||||||||
| jmaeng-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.1803 | 96.5537 | 97.8151 | 57.7486 | 17062 | 609 | 17057 | 381 | 365 | 95.8005 | |
| jmaeng-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.1803 | 96.5537 | 97.8151 | 57.7486 | 17062 | 609 | 17057 | 381 | 365 | 95.8005 | |
| anovak-vg | SNP | ti | map_l125_m2_e1 | het | 77.5988 | 89.9303 | 68.2413 | 78.1425 | 17165 | 1922 | 17046 | 7933 | 1721 | 21.6942 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 88.1261 | 88.9650 | 87.3028 | 53.9810 | 15721 | 1950 | 17045 | 2479 | 1231 | 49.6571 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 88.1261 | 88.9650 | 87.3028 | 53.9810 | 15721 | 1950 | 17045 | 2479 | 1231 | 49.6571 | |
| gduggal-snapplat | SNP | * | map_l125_m0_e0 | * | 91.0834 | 87.8360 | 94.5802 | 84.8287 | 17027 | 2358 | 17032 | 976 | 546 | 55.9426 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 97.3219 | 95.4262 | 99.2945 | 64.0832 | 17004 | 815 | 17030 | 121 | 44 | 36.3636 | |
| qzeng-custom | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.6848 | 99.5401 | 99.8300 | 56.5387 | 17098 | 79 | 17030 | 29 | 9 | 31.0345 | |
| mlin-fermikit | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.2029 | 96.8864 | 99.5557 | 62.5968 | 17021 | 547 | 17030 | 76 | 4 | 5.2632 | |
| ckim-vqsr | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.5470 | 99.1558 | 99.9413 | 57.3410 | 17032 | 145 | 17028 | 10 | 8 | 80.0000 | |
| ciseli-custom | SNP | ti | map_l100_m0_e0 | * | 82.2845 | 78.2555 | 86.7509 | 73.7443 | 17037 | 4734 | 17024 | 2600 | 753 | 28.9615 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.1456 | 97.0290 | 99.2882 | 49.3199 | 17146 | 525 | 17018 | 122 | 80 | 65.5738 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.1456 | 97.0290 | 99.2882 | 49.3199 | 17146 | 525 | 17018 | 122 | 80 | 65.5738 | |
| astatham-gatk | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.5088 | 99.0743 | 99.9471 | 55.8025 | 17018 | 159 | 17015 | 9 | 6 | 66.6667 | |
| ciseli-custom | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 86.4138 | 96.3627 | 78.3270 | 66.2442 | 16929 | 639 | 17004 | 4705 | 98 | 2.0829 | |
| ltrigg-rtg1 | SNP | ti | HG002compoundhet | * | 98.6394 | 97.4883 | 99.8180 | 33.8383 | 17039 | 439 | 17003 | 31 | 12 | 38.7097 | |
| gduggal-bwaplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 92.0166 | 86.7307 | 97.9886 | 88.3681 | 16981 | 2598 | 17002 | 349 | 101 | 28.9398 | |
| gduggal-bwaplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 92.0166 | 86.7307 | 97.9886 | 88.3681 | 16981 | 2598 | 17002 | 349 | 101 | 28.9398 | |
| gduggal-bwaplat | SNP | * | segdup | het | 98.4496 | 98.0539 | 98.8484 | 95.2313 | 16980 | 337 | 16996 | 198 | 12 | 6.0606 | |
| gduggal-bwafb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 92.2413 | 93.5539 | 90.9650 | 64.4972 | 16995 | 1171 | 16995 | 1688 | 1649 | 97.6896 | |
| gduggal-bwafb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 92.2413 | 93.5539 | 90.9650 | 64.4972 | 16995 | 1171 | 16995 | 1688 | 1649 | 97.6896 | |
| asubramanian-gatk | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.2719 | 98.8007 | 99.7476 | 56.4979 | 16971 | 206 | 16992 | 43 | 6 | 13.9535 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 96.7435 | 96.0727 | 97.4237 | 57.9207 | 16977 | 694 | 16979 | 449 | 417 | 92.8731 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 96.7435 | 96.0727 | 97.4237 | 57.9207 | 16977 | 694 | 16979 | 449 | 417 | 92.8731 | |
| qzeng-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 95.7239 | 96.8194 | 94.6529 | 42.8294 | 10076 | 331 | 16976 | 959 | 707 | 73.7226 | |
| gduggal-snapplat | SNP | ti | map_l100_m2_e0 | homalt | 96.2308 | 92.8014 | 99.9235 | 62.6446 | 16991 | 1318 | 16974 | 13 | 13 | 100.0000 | |
| ghariani-varprowl | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 85.8608 | 77.6154 | 96.0663 | 66.4017 | 16997 | 4902 | 16973 | 695 | 593 | 85.3237 | |
| jpowers-varprowl | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 85.9015 | 77.6154 | 96.1682 | 66.3211 | 16997 | 4902 | 16966 | 676 | 597 | 88.3136 | |
| cchapple-custom | SNP | * | map_l125_m2_e1 | homalt | 98.3624 | 96.7830 | 99.9941 | 64.4456 | 16968 | 564 | 16962 | 1 | 1 | 100.0000 | |
| qzeng-custom | SNP | * | segdup | het | 98.3153 | 98.7007 | 97.9329 | 93.6755 | 17092 | 225 | 16961 | 358 | 11 | 3.0726 | |
| astatham-gatk | SNP | * | map_l100_m0_e0 | het | 88.7308 | 80.0000 | 99.6007 | 77.5238 | 16964 | 4241 | 16960 | 68 | 23 | 33.8235 | |
| gduggal-bwaplat | SNP | * | map_l150_m2_e0 | * | 69.3373 | 53.2274 | 99.4313 | 91.0275 | 16954 | 14898 | 16958 | 97 | 30 | 30.9278 | |
| gduggal-snapvard | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 93.0446 | 97.3019 | 89.1441 | 72.7080 | 17094 | 474 | 16957 | 2065 | 141 | 6.8281 | |
| gduggal-bwavard | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.2565 | 97.5239 | 96.9905 | 69.1218 | 17133 | 435 | 16952 | 526 | 189 | 35.9316 | |
| anovak-vg | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 62.7686 | 68.2214 | 58.1230 | 35.1882 | 8542 | 3979 | 16951 | 12213 | 9571 | 78.3673 | |
| ghariani-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 62.8376 | 94.6349 | 47.0342 | 60.4447 | 16863 | 956 | 16945 | 19082 | 18800 | 98.5222 | |
| hfeng-pmm1 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.8880 | 99.8233 | 99.9528 | 71.8323 | 16945 | 30 | 16945 | 8 | 5 | 62.5000 | |
| hfeng-pmm1 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.8880 | 99.8233 | 99.9528 | 71.8323 | 16945 | 30 | 16945 | 8 | 5 | 62.5000 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 82.8608 | 81.8751 | 83.8705 | 37.8607 | 16863 | 3733 | 16941 | 3258 | 3048 | 93.5543 | |
| ltrigg-rtg1 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.5807 | 99.2754 | 99.8880 | 68.6524 | 16852 | 123 | 16941 | 19 | 8 | 42.1053 | |
| ltrigg-rtg1 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.5807 | 99.2754 | 99.8880 | 68.6524 | 16852 | 123 | 16941 | 19 | 8 | 42.1053 | |
| eyeh-varpipe | SNP | * | HG002compoundhet | * | 97.2195 | 99.1054 | 95.4041 | 44.2893 | 25591 | 231 | 16939 | 816 | 176 | 21.5686 | |
| hfeng-pmm2 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.8615 | 99.7820 | 99.9410 | 72.3104 | 16938 | 37 | 16938 | 10 | 6 | 60.0000 | |
| hfeng-pmm2 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.8615 | 99.7820 | 99.9410 | 72.3104 | 16938 | 37 | 16938 | 10 | 6 | 60.0000 | |
| gduggal-snapfb | SNP | tv | map_siren | homalt | 98.9049 | 98.2309 | 99.5884 | 65.8705 | 16935 | 305 | 16935 | 70 | 12 | 17.1429 | |
| ckim-dragen | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.5364 | 99.2047 | 99.8702 | 65.5442 | 16840 | 135 | 16932 | 22 | 12 | 54.5455 | |
| ckim-dragen | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.5364 | 99.2047 | 99.8702 | 65.5442 | 16840 | 135 | 16932 | 22 | 12 | 54.5455 | |
| hfeng-pmm3 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.8555 | 99.7467 | 99.9646 | 71.3411 | 16932 | 43 | 16932 | 6 | 3 | 50.0000 | |
| hfeng-pmm3 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.8555 | 99.7467 | 99.9646 | 71.3411 | 16932 | 43 | 16932 | 6 | 3 | 50.0000 | |
| astatham-gatk | SNP | * | segdup | het | 98.7752 | 97.7998 | 99.7702 | 91.3893 | 16936 | 381 | 16930 | 39 | 2 | 5.1282 | |