UKBB GWAS Manifest 20170915
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Summary stat output explantion
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https://github.com/Nealelab/UK_Biobank_GWAS/blob/master/README.md#summary-stat-output
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NOTE: Variants are listed in the form CHR:POS:REF:ALT, where the ALT allele is the effect allele in the model
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NOTE: The ALT allele is NOT always the minor allele, but the non-reference allele as stated in the UK Biobank ukb_mfi_chr*_v2.txt and our variants.tsv file
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QC-positive Sample ID list (ukb_sqc_v2.nealelab_UKBBqc_n377199.id.tsv.gz)
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ColumnsDescription
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ID_1Generic ID from ukb_sqc_v2.txt file
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ID_2Generic ID from ukb_sqc_v2.txt file
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Submitted.Plate.namePlate Name from ukb_sqc_v2.txt file
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Submitted.WellWell position ID from ukb_sqc_v2.txt file
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QC-positive SNP map file (variants.tsv)
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ColumnsDescription
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variant (hg19) [CHROM:POS:REF:ALT]Variant position as [Chromosome : hg19 Position : reference allele : alternate allele]
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rsidSNP rsID as provided by UK Biobank
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infoSNP INFO score as provided by UK Biobank
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AF
SNP alternate allele frequency (NOT always minor allele frequency) from 337,199 QC-positive samples
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pHWEHardy-Weinberg p-value from 337,199 QC-positive samples
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callRateGenotyping call rate from 337,199 QC-positive samples
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Summary statistic file ([FieldID].assoc.tsv.gz)
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ColumnsDescription
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variant (hg19) [CHROM:POS:REF:ALT]Variant position as [Chromosome : hg19 Position : reference allele : alternate allele]
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rsidSNP rsID as provided by UK Biobank
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nCompleteSamplesNumber of samples analyzed with non-missing phenotypes
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ACDosage allele count from all samples with non-missing phenotypes
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ytx
Dosage alternate allele count (ytx means "y * x" where y=phenotype and x=alternate allele dosage)
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betalinear regression beta coefficient
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selinear regression standard error
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pvallinear regression p-value
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