I’ve recalled the SNPs for my Helianthus exilis population genetics for a third time. This time I’m using GATK. This is aligned using BWA to the Nov22k22 reference.
This is two plates of GBS (96-plex each) plus 34 H. annuus samples from G. Baute (also 96-plex GBS). Three exilis samples were removed because they had little or no reads. Reads were trimmed for adapters and quality using trimmomatic (and the number of reads kept after trimming are used here).
So, there is a relationship between number of reads and resulting heterozygosity. It makes some sense because you need a higher number of reads to call a heterozygote than a homozygote. It’s not as bad as what was happening when we were calling snps using the maximum likelihood script. Using a linear model, number of reads accounts for %16 of the variation in heterozygosity.
If you compare this to my previous posts, the heterozygosity is vastly lower for all samples. That is because I previously looked at variable sites with a certain amount of coverage, and here are all sites. So a majority of these sites are invariant.