Variant sites (alt >= 25% at informative depth >= 4 in any oyster): 46
  seen in >= 2 oysters: 12
  differ between Qui vs Rio (pooled alt-frequency difference >= 0.5): 10  [CpG-destroying: 3]
    2087061 C>A  Pum=  Qui=0.0  Rio=1.0
    2087305 T>G  Pum=0.5  Qui=0.0  Rio=0.759
    2087419 A>G  Pum=0.6  Qui=0.0  Rio=0.774
    2087437 C>T  Pum=  Qui=0.0  Rio=1.0
    2087474 C>T  Pum=  Qui=0.0  Rio=1.0
    2087477 A>T  Pum=0.667  Qui=0.0  Rio=0.667
    2087540 A>G  Pum=0.636  Qui=0.0  Rio=0.655
    2087565 A>G  Pum=0.6  Qui=0.0  Rio=0.607
    2087648 C>T  Pum=  Qui=0.0  Rio=1.0
    2087892 C>A  Pum=  Qui=0.0  Rio=1.0

11 CpGs in target; 7 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    55.6     45        1    5.5
Qui1     Qui    95.7     46        0    7.0
Qui2     Qui    91.4     35        0    8.9
Qui3     Qui   100.0     30        0    8.4
Qui4     Qui    91.4     35        0    6.4
Rio1     Rio    50.9     55        3    7.5
Rio2     Rio    59.5     42        2    4.6
Rio3     Rio    66.7     27        1    4.1
Rio4     Rio    61.3     31        0    6.3