Variant sites (alt >= 25% at informative depth >= 4 in any oyster): 50
  seen in >= 2 oysters: 25
  differ between Qui vs Rio (pooled alt-frequency difference >= 0.5): 9  [CpG-destroying: 4]
    62502023 C>T  Pum=0.0  Qui=0.5  Rio=0.0
    62502172 A>C  Pum=0.571  Qui=0.242  Rio=0.826
    62502184 C>T  Pum=0.75  Qui=0.3  Rio=0.882
    62502373 C>A  Pum=0.429  Qui=0.5  Rio=0.0
    62502376 T>A  Pum=0.5  Qui=0.128  Rio=0.696
    62502401 A>T  Pum=0.429  Qui=0.5  Rio=0.0
    62502565 C>T  Pum=0.8  Qui=0.529  Rio=0.0
    62502880 G>A  Pum=  Qui=0.231  Rio=0.75
    62502895 T>C  Pum=0.375  Qui=0.615  Rio=0.0

23 CpGs in target; 2 testable for SNPs (>= 8 pooled genotype reads at C and G in each of Qui, Rio)
sample   pop   meth%  calls CtoT_snp  depth
Pum1     Pum    51.6     31        2    6.4
Qui1     Qui    64.3     84        2   10.2
Qui2     Qui    63.2     38        2    8.7
Qui3     Qui    37.7     53        1   11.0
Qui4     Qui    57.7     52        2    8.6
Rio1     Rio    85.7     21        1    8.8
Rio2     Rio    85.7     28        2    7.2
Rio3     Rio    87.5     32        1    4.9
Rio4     Rio    82.9     35        2    6.1