Variant sites (alt >= 25% at informative depth >= 4 in any oyster): 46
  seen in >= 2 oysters: 20
  differ between Qui vs Rio (pooled alt-frequency difference >= 0.5): 13  [CpG-destroying: 3]
    54887065 T>A  Pum=0.75  Qui=1.0  Rio=0.1
    54887085 A>T  Pum=  Qui=0.895  Rio=0.098
    54887105 A>T  Pum=  Qui=1.0  Rio=0.116
    54887116 A>G  Pum=0.75  Qui=0.88  Rio=0.14
    54887132 A>T  Pum=0.0  Qui=1.0  Rio=0.143
    54887151 A>G  Pum=0.143  Qui=0.867  Rio=0.128
    54887218 G>A  Pum=0.0  Qui=0.971  Rio=0.222
    54887249 A>G  Pum=0.0  Qui=0.829  Rio=0.216
    54887266 G>A  Pum=0.0  Qui=1.0  Rio=0.265
    54887516 T>A  Pum=0.083  Qui=1.0  Rio=0.333
    54887846 A>G  Pum=0.0  Qui=0.958  Rio=0.263
    54887925 T>A  Pum=0.062  Qui=1.0  Rio=0.378
    54888000 C>T  Pum=0.0  Qui=1.0  Rio=0.154

9 CpGs in target; 1 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    85.1     67        0   12.1
Qui1     Qui    36.8     19        0    4.4
Qui2     Qui    60.7     61        0    8.6
Qui3     Qui    68.8     48        0    7.6
Qui4     Qui    60.3     58        0    6.2
Rio1     Rio    85.1     67        0   11.0
Rio2     Rio    95.0    101        0   11.3
Rio3     Rio    82.1     84        0    8.7
Rio4     Rio    94.3     53        0    9.9