Calculating allelic mismatch between technical replicates
We calculated the proportion of shared alleles between technical
replicates for all specimens using custom scripts (see Data
Accessibility) and conducted this assessment using both the probe and
contig SNP datasets. We required replicates to share at least 200
biallelic SNPs (400 alleles) with no missing data and sorted allelic
mismatches for a given SNP into those with different homozygous calls
(two allele differences) and those related to different
heterozygous/homozygous calls (one allele difference). Further, in cases
of heterozygous mismatches, we identified which replicate was
heterozygous and which was homozygous (e.g., supernatant vs. RADseq).
The number of samples in each comparison is shown in Table 2.