Variant sites (alt >= 25% at informative depth >= 4 in any oyster): 55
  seen in >= 2 oysters: 31
  differ between Qui vs Rio (pooled alt-frequency difference >= 0.5): 17  [CpG-destroying: 5]
    55561195 C>T  Pum=0.875  Qui=0.833  Rio=0.059
    55561202 T>A  Pum=0.778  Qui=0.769  Rio=0.079
    55561219 T>A  Pum=0.889  Qui=0.833  Rio=0.048
    55561221 A>C  Pum=0.778  Qui=0.684  Rio=0.048
    55561239 C>T  Pum=0.75  Qui=0.722  Rio=0.079
    55561258 A>T  Pum=0.7  Qui=0.696  Rio=0.048
    55561337 T>C  Pum=0.9  Qui=0.897  Rio=0.024
    55561382 C>T  Pum=1.0  Qui=1.0  Rio=0.111
    55561469 A>G  Pum=0.444  Qui=0.619  Rio=0.0
    55561519 T>A  Pum=1.0  Qui=0.87  Rio=0.143
    55561526 T>A  Pum=0.625  Qui=0.739  Rio=0.161
    55561544 A>T  Pum=1.0  Qui=0.962  Rio=0.207
    55561623 C>T  Pum=1.0  Qui=0.941  Rio=0.167
    55561646 T>G  Pum=0.692  Qui=0.5  Rio=0.0
    55561780 T>A  Pum=1.0  Qui=0.955  Rio=0.077
    55561882 G>A  Pum=  Qui=1.0  Rio=0.071
    55561932 A>G  Pum=0.5  Qui=0.5  Rio=0.0

14 CpGs in target; 10 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    65.2     69        1    7.3
Qui1     Qui    80.0     35        1    5.4
Qui2     Qui    47.1     17        1    3.8
Qui3     Qui    58.9     56        1    6.1
Qui4     Qui    43.3     30        1    5.3
Rio1     Rio     2.7     37        0    8.8
Rio2     Rio     2.6     38        0    8.6
Rio3     Rio     0.0     28        1    5.0
Rio4     Rio     0.0     29        0    9.9