For raw reads of this publication, you need to go to the short read archive (SRA) and search for the following identifiers: 1. cluhar_rc6_codingGene_GOonGene.gff.gz File with gene annotations in the herring genome. For a detailed description of the methods, please, check our publication. The file is provided in GFF format version 3 (http://gmod.org/wiki/GFF3). We merged our GO annotations (Ontology_term) together with other attributes. 2. Individual.GATK.filtered.only.SNPs.vcf.gz File with the VCF genotype calls for the 16 individuals (8 Baltic + 8 Atlantic) analysed in the paper. The individual SNP calls were generated with GATK Unified Genotyper and the output format is version 4.1 (https://samtools.github.io/hts-specs/VCFv4.1.pdf). We also did some additional filtering as specified in the header of the file: ##FILTER= 1000"> and finally, removed indels from the file. 3. Pool_20.filtered.vcf.gz File with the VCF variants for the 20 pools of populations (see the paper for a detailed description) analysed. The population SNP calls were generated with GATK Unified Genotyper and the output format is version 4.1 (https://samtools.github.io/hts-specs/VCFv4.1.pdf). We continued doing some additional filtering as specified in the header of the file: ##FILTER= 60.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0|| DP < 100"> and finally, removed indels from the file.