Variant sites (alt >= 25% at informative depth >= 4 in any oyster): 55
  seen in >= 2 oysters: 12
  differ between Qui vs Rio (pooled alt-frequency difference >= 0.5): 8  [CpG-destroying: 3]
    59258164 C>A  Pum=  Qui=0.895  Rio=0.077
    59258274 C>T  Pum=0.75  Qui=0.857  Rio=0.2
    59258290 C>T  Pum=  Qui=0.824  Rio=0.188
    59258376 T>A  Pum=0.455  Qui=0.759  Rio=0.182
    59258434 C>T  Pum=0.4  Qui=0.76  Rio=0.08
    59258455 T>A  Pum=0.286  Qui=0.594  Rio=0.049
    59258601 G>T  Pum=  Qui=0.867  Rio=0.15
    59258608 A>T  Pum=0.25  Qui=0.795  Rio=0.143

28 CpGs in target; 11 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    37.0     81        1    8.8
Qui1     Qui    34.3     70        0    6.8
Qui2     Qui    49.1    108        1    8.1
Qui3     Qui    89.7    107        1    8.3
Qui4     Qui    69.2     39        0    4.8
Rio1     Rio     1.9    105        0    8.7
Rio2     Rio     4.2     48        0    5.6
Rio3     Rio     0.0     51        0    5.0
Rio4     Rio     0.0     77        1    6.4