Full output GWAS female

We infected female flies from 94 of the DGRP lines with 104 plaque-forming units (PFU) WNV-Kun by intrathoracic injection and determined their mortality rates as compared to flies treated with buffer only (mock infection). We monitored survival daily for 30 days and calculated the hazard ratio as a metric of survival. We then used the log of the hazard ratio as the quantitative phenotype for the GWAS, as described (Chow et al., 2013).

Column definitions are as follows:
chr – chromosome numbers
rs – SNP IDs
ps – basepair positions on the chromosome
n_miss – number of missing individuals for a given SNP
allele1 – minor allele
allele0 – major allele
af – allele frequency
beta – beta estimates
se – standard errors for beta
l_remle – restricted maximum likelihood estimates for lambda
l_mle – maximum likelihood estimates for lambda
p_wald – p values from Wald test
p_lrt – p values from likelihood-ratio test
p_score – p values from Score test