Variant sites (alt >= 25% at informative depth >= 4 in any oyster): 27
  seen in >= 2 oysters: 10
  differ between Qui vs Rio (pooled alt-frequency difference >= 0.5): 9  [CpG-destroying: 2]
    130913044 A>G  Pum=0.0  Qui=0.767  Rio=0.0
    130913050 A>G  Pum=0.0  Qui=0.767  Rio=0.0
    130913124 A>C  Pum=0.0  Qui=0.824  Rio=0.0
    130913141 G>A  Pum=0.0  Qui=1.0  Rio=0.0
    130913182 G>A  Pum=0.0  Qui=1.0  Rio=0.0
    130913254 A>T  Pum=0.0  Qui=0.806  Rio=0.0
    130913343 A>G  Pum=0.0  Qui=0.857  Rio=0.0
    130913643 A>T  Pum=0.0  Qui=0.606  Rio=0.0
    130913971 A>C  Pum=0.0  Qui=0.723  Rio=0.0

11 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    95.8     71        0    8.2
Qui1     Qui    79.4     63        1    9.3
Qui2     Qui    50.0     64        0    8.7
Qui3     Qui    61.9     84        0   11.2
Qui4     Qui    61.8     55        0    5.1
Rio1     Rio    97.0     67        0   10.6
Rio2     Rio    98.0     51        0    6.7
Rio3     Rio    93.9     49        0    6.8
Rio4     Rio    98.2     57        0    8.4