Comparison of results for the following data after removing outlier samples

1. Filter4: Data obtained post BLAST filter, low read filter and low coverage filter
2. Filter 5a: Data obtained post filter4 AND removing problematic loci identified by rad_haplotyper
3. Filter 5b: Data obtained post filter4 AND keeping only those loci that remain after full SNP filtering pipeline

Outliers removed: PBF_158, WOF_232, WOF_236 and WOB_41.

Filter#	Number of loci	Methylation cutoff
4	7006	-2.822
5a	6101	-2.863801
5b	5579	-2.870767

Result1: MDS without outliers

Filter4	Filter5a	Filter5b

Result2: Methylation heatmap clustered by rows and columns without outliers

Filter4	Filter5a	Filter5b

Result3: %Methylation without outliers

Filter4	Filter5a	Filter5b

Result5a: Pst

	Filter4	Filter5a	Filter5b
Mean Pst	0.054	0.059	0.061

Filter4	Filter5a	Filter5b

Result5b: Pairwise Pst

Table 1 Filter4	Table 2 Filter5a	Table3 Filter5b
EOB PBF WOB WOF EOB x 0.046 0.077 0.03 PBF x 0.064 0.033 WOB x 0.079 WOF x	EOB PBF WOB WOF EOB x 0.046 0.083 0.028 PBF x 0.067 0.035 WOB x 0.085 WOF x	EOB PBF WOB WOF EOB x 0.047 0.085 0.029 PBF x 0.065 0.038 WOB x 0.085 WOF x

Result5c: Pooled Back Reef vs Pooled Fringe Reef Pst

	Filter4	Filter5a	Filter5b
Mean Pst	0.017	0.017	0.016