Data from: Limited evidence for extensive genetic differentiation between X and Y chromosomes in Hybognathus amarus (Cypriniformes:Leuciscidae)

We used Nextera-tagmented reductively amplified DNA (nextRAD) sequencing
data to discover SNPs in Rio Grande silvery minnow samples of known and
unknown sex; and we produced two contig level genomes from Nanopore
long-read sequencing. Raw NextRAD was aligned to each of the genomes.
Subsequent SNP calling and filtering were repeated independently to obtain
two datasets, one using the female genome as reference (female-referenced
dataset) and another using the male genome (male-referenced dataset). The
SNP calling identified 4.46 M raw variants in female-referenced dataset
and of these 16,714 biallelic SNPs were retained after all filtering
steps. For this set of SNPs, the average depth of coverage for the
retained 64 females was 35.81 (ranging from 8.94 to 86.88) and 33.14 for
the retained 53 males (ranging from 18.93 to 65.56). When using the male
genome as reference we obtained 3.77 M raw variants and 17,920 biallelic
SNPs. In this case the average depth of coverage for the same 64 females
was 36.01 (ranging from 8.99 to 87.34) and for the same 53 males was 33.36
(ranging from 19.23 to 66.27).