Table S1

Tab-delimited text file with the position, alleles, alternative frequencies within morphs, F-statistics between morphs and samples and predicted effect of the variant on protein composition for all the variants after the final filtering step.
id: Identifier for each variant from 1 to 19,252transcript_id: Name of the transcript from the Trinity assembly.start: Start position of polymorphism within contig.end: End position of polymorphism within contig.ref: Base(s) of the reference allele.alt: Base(s) of the alternative allele.var_pos: Position of polymorphism within contig.NCBI_id: Sequence identifier for chromosome or scaffold in genome.Chr: Name of chromosome.Chr_pos: Position mapped to in chromosome.Freq_LB: Frequency of alternative allele within the LB morph.Freq_PL: Frequency of alternative allele within the PL morph.Freq_SB: Frequency of alternative allele within the SB morph.Fst: Estimate of F ST between morphs.Fpt: Estimate of F P T or variation among samples (pools). See methods for further explanation.effect: Which effect does the mutation have on the gene, 3’- and 5’ UTR indicate mutations in those regions, synonymousdo not change the reading frame but mutations that do so are coded as transitions from one amino acid to another (single letter a.a. code)gene_name: Gene name based on SalmonBase annotation.