Genome-enabled analysis of population dynamics and virulence associated loci in the oat crown rust fungus Puccinia coronata f. sp. avenae

These are VCF files that represent genomic variation of 182 to 217 Puccinia coronata f. sp. avenae isolates from the US against three genome references. Raw Illumina sequencing reads of 162 US and South African isolates used in this study are available in the NCBI BioProject PRJNA660269. Reads of 62 US isolates used in this study generated by Miller et al., (2020 - https://doi.org/10.25919/k0ze-ya06) are available in the NCBI BioProject PRJNA398546.\nLineage: Details about data acquisition can be found in publication Hewitt et al., (2023). After processing of DNA short reads from all isolates.Trimmed FASTQ files were aligned independently to the reference genomes (12SD80 and 12NC29 primary contigs, Pca203 diploid and haploid chromosomes) using the ‘bwa mem’ algorithm of BWA (v0.7.71). BAM files were processed with SAMtools (v1.12) and Picard (v2.26.9), including removal of duplicate reads and relabelling of reads by sample. Variant calling was performed separately for each reference using FreeBayes (v1.3.5) with option ‘--use-best-n-alleles 6’ and subsequent VCF files were filtered using vcffilter of vcflib (v1.0.1) with the parameters ‘QUAL > 20 & QUAL/AO > 10 & SAF > 0 & SAR > 0 & RPR > 1 & RPL > 1 & AC > 0.’