(Unless the phenotype is quantitative instead of case/control then phenotypes are ignored and FRQ_A and FRQ_U are both equal to the overall FRQ value.). If the 'case-control-freqs' modifier is present, the FRQ column is replaced with FRQ_A and FRQ_U columns reporting case and control frequencies, respectively, and NCHROBS will not include missing-phenotype samples. Standard error of effect (not odds ratio) estimate Regression coefficient (for quantitative traits) or odds ratio R-squared quality metric/information content assoc.dosage (dosage association analysis report)Ī text file with a header line, and then usually one line per variant with the following 8-10 fields: CHR xy has also been specified, there are three additional fields at the end: SEīottom of xy% symmetric approx. If the 'counts' modifier is present, the 5th and 6th fields are replaced with: C_A Odds(allele 1 | case) / odds(allele 1 | control) Not present with 'fisher'/'fisher-midp' modifier. Produced by -assoc acting on a case/control phenotype.Ī text file with a header line, and then one line per variant typically with the following 9-10 fields: CHRĪllelic test chi-square statistic. assoc.fisher (case/control association allelic test report)
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