Table 2. Summary of number of SNPs.

Analysis Step	Host	Symbiont
(A) Filtered vcf File
Total number of SNPs	1,808	59
High Outlier SNPs	84	4
Neutral SNPs	1,637	52
(B) Filtered 1 SNP per Contig File
High Outlier SNPs	66	4
Neutral SNPs	279	20

Note:

Summary of the number of SNPs after original filtering using vcftools (A) and after filtering to include only one SNP per contig as in the dDocent pipeline (B). Filtering for 1 SNP per contig was done after original filtering using vcftools and separating neutral and high outlier loci. Number of SNPs are included for the host (VA-B, VA-W, RI-B, RI-W) and symbiont (VA-B and RI-B) analyses discussed here.