Increased virulence of Puccinia coronata f. sp. avenae populations through allele frequency changes at multiple putative Avr loci.

These are VCF files that represent genomic variation of 60 Puccinia coronata f. sp. avenae isolates against two genome references. Raw Illumina sequencing reads used in this study are available in the NCBI BioProject PRJNA398546. \nLineage: Details about data acquisition can be found in publication Miller et al 2020. After processing of DNA short reads from all isolates. Trimmed FASTQ files were aligned to the 12SD80 or 12NC29 primary contig reference genomes of P. coronata f. sp. avenae with BWA-MEM (v0.7.15) using default parameters. The SAM output from BWA-MEM was piped directly to SAMtools (v1.5) for conversion to BAM format, sorting, PCR duplicate removal, and indexing. Freebayes was used to produce SNP data. All resulting VCF files were quality filtered with vcffilter in vcflib (v1.0.0-rc1, commit 717cfbf) with the parameters QUAL > 20 & AC > 0, and then the representations of the variants were regularized by using vcfallelicprimitives in vcflib as representations of variants that differ between methods.