VCF files of industrial yeasts

Results of GATK genome analysis, used for allele frequency plots.<br>Newly generated FASTQ sequencing files along with those obtained from SRA were trimmed and filtered using fastp (Chen et al., 2018), and mapped to the S288C reference genome (R64.2.1.) downloaded from the SGD database (yeastgenome.org) and the reference genomes of the other Saccharomyces species (Scannell et al., 2011), using bwa 0.7.17. (Li and Durbin, 2009). Sorted BAM files were obtained using samtools 1.7. (Li et al., 2009) and Picard-tools 1.124. (http://picard.sourceforge.net) was used to mark duplicated reads. Local realignment around indels and joint variant calling and filtering for the six samples were performed with GATK 4.1.6.0 (Auwera et al., 2013; Poplin et al., 2018) with regions annotated in the SGD database as simple repeats, centromeric regions, telomeric regions, or LTRs excluded. First, genomic VCF files were obtained, joint calling was applied, and in the resulting VCF files, only SNPs were selected. SNPs were filtered according to the parameters used by (Fay et al., 2019): QD &lt; 5.0; QUAL &lt; 30.0; SOR &gt; 3.0; FS &gt; 60.0; MQ &lt; 40.0; MQRankSum &lt; -12.5; ReadPosRankSum &lt; -8.0; --set-filtered-genotype-to-no-call true.<br>