Structural and nucleotide diversity at the Avr1a locus among 31 isolates of Phytophthora sojae reveal distinct haplotypes associated with virulence phenotypes. a Variants in the vicinity of the Phytophthora sojae Avr1a gene. The yellow box represents the coding region of the gene. The orange box shows the location of the deletion. Asterisks (*) indicate approximate positions of the SNPs. Those SNPs are representative of a cluster of SNPs defining a haplotype. b Schematic graph of the position of the SNPs for each isolate, grouped by haplotypes. SNPs in gray background are different from the reference genome (isolate P6497). c Phenotypic response of the outliers (when the phenotype did not match the genotype based on the hypocotyl test) from the hydroponic assay. Responses showed here are representative of all isolates tested. All phenotypic responses of other tested isolates can be found in Additional file 2. CNV of Avr1a gene for the reference genome (P6497) is based on results from Qutob et al.