Aquila chrysaetos SNPs

This file describes SNPs identified in adult and juvenile golden eagles (including scaffold, SNP location, major/minor alleles, allele frequencies and more). We used Trimmomatic 0.35 to remove adaptors and discard low quality bases from pooled sequencing reads. Reads were scanned using a 4 bp window and cut whenever the average phred quality score dropped below 20. Reads less than 40 bases long were subsequently discarded. High-quality reads were mapped to the relevant genome using BWA 0.7.13. We subsequently used Picard to merge male and female reads within each life stage group (i.e., nestling or adult) to increase coverage, as well as remove duplicate reads. Samtools was used to remove ambiguously mapped reads (e.g., reads with mapping quality below 20) and generate a mpileup file. PoPoolation2 was used to filter indels, identify SNPs and calculate allele frequencies. When calculating allele frequencies, we discarded SNPs with a minor allele frequency below 2, a minimum coverage below 15 for either cohort, or a maximum coverage greater than 99. See README file for additional information