Table 3 Number of SNPs retained after each filtering step for the black-lip rock oyster, Saccostrea echinata
Step | SNP count (number samples) |
|---|---|
Stacks catalogue | 15,674,503 (282 samples) |
Genotyped | |
  > 70% of the samples | 44,904 (282 samples) |
  > 50% of the locations | |
 HOBS < 0.5 | |
 Local MAF > 0.01 | |
 Loci < 2 alleles | 35,811 |
QC in R | |
 VCF conversion | 35,152 |
 Missing per SNP < 70% | 27,887 (280 samples) |
 Missing per individual < 50% | 27,887 (272 samples) |
Outlier detection | |
 BAYESCAN outliers | 51 |
 PCAdapt outliers | 483 |
 Outliers identified with both methods | 31 |
 Putatively neutral | 27,856 |