Variant sites (alt >= 25% at informative depth >= 4 in any oyster): 59
  seen in >= 2 oysters: 40
  differ between Qui vs Rio (pooled alt-frequency difference >= 0.5): 13  [CpG-destroying: 1]
    62509297 G>A  Pum=  Qui=0.227  Rio=0.818
    62509361 A>G  Pum=0.714  Qui=0.491  Rio=1.0
    62509663 A>T  Pum=0.364  Qui=0.071  Rio=0.652
    62509703 A>T  Pum=0.222  Qui=0.0  Rio=0.667
    62509708 T>A  Pum=0.444  Qui=0.214  Rio=0.857
    62509709 T>A  Pum=0.444  Qui=0.25  Rio=1.0
    62509710 T>A  Pum=0.444  Qui=0.25  Rio=1.0
    62509711 T>A  Pum=0.444  Qui=0.207  Rio=1.0
    62509712 T>A  Pum=0.444  Qui=0.207  Rio=0.929
    62509713 T>A  Pum=0.571  Qui=0.2  Rio=0.929
    62509714 T>A  Pum=0.571  Qui=0.241  Rio=0.929
    62509757 A>G  Pum=0.2  Qui=0.091  Rio=0.875
    62509988 A>C  Pum=0.571  Qui=0.086  Rio=0.667

16 CpGs in target; 9 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    25.5     47        1    6.9
Qui1     Qui    29.7     64        1    7.4
Qui2     Qui    20.2     89        2    9.8
Qui3     Qui    18.4    114        2   13.6
Qui4     Qui    21.5     65        3    8.4
Rio1     Rio    48.5     33        0    4.6
Rio2     Rio    37.8     74        0    6.2
Rio3     Rio    37.2     43        1    4.4
Rio4     Rio    41.9     43        1    7.3