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Table 3 Number of SNPs retained after each filtering step for the black-lip rock oyster, Saccostrea echinata

From: Mitochondrial and nuclear genetic analyses of the tropical black-lip rock oyster (Saccostrea echinata) reveals population subdivision and informs sustainable aquaculture development

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