Extended Data Fig. 2: Mapping of sequencing reads and genome-wide methylome levels.
From: Epigenetic divergence during early stages of speciation in an African crater lake cichlid fish
a. Mapping rates (percentage total reads) for RRBS and WGBS sequencing reads aligned to the SNP-corrected Maylandia zebra reference assembly (GCF_000238955.4 M_zebra_UMD2a). Black midlines and whiskers represent median values with 95% CI of mapping rates for each population. Overall mapping rates are shown at the bottom of each graph (mean ± sd). b. Upper panel: Genome-wide average liver methylation levels for each sample of each population (B, benthic, L, littoral and R, river; w, wild-caught). Average mCG/CG levels in non-overlapping 1kbp-long windows. Median and mean values are indicated with black midlines and white dots, respectively. Lower panel: CG coverage (count of unique mapped reads) of all WGBS samples. c. Boxplots showing PC scores for PC1 and PC2 associated with the PC analysis (Fig.1a) of RRBS-related genome-wide CG methylation variation among all populations. Statistical report for MANOVA test is shown at the bottom of the graph and post-hoc Games-Howell multiple comparison two-sided P-values adjusted with the Tukey’s method are shown for each pairwise comparison above each boxplot. n ≥ 2 and n ≥ 11 biological replicates for WGBS and RRBS datasets, respectively, for all graphs. All box plots indicate median (middle line), 25th, 75th percentile (box), and 5th and 95th percentile (whiskers) as well as outliers (single points).
