Skip to main content

Table 1 Filtering steps and SNPs counts retained after each step

From: Fine-scale population structure and evidence for local adaptation in Australian giant black tiger shrimp (Penaeus monodon) using SNP analysis

Steps

Retained SNP count

Initial potential SNPs

126,511

Average read depth of ≥7

126,511

Replication average ≥ 0.9

122,037

Call rate of ≥80%

23,845

Similar sequence clusters of ≤0.95

19,328

Minor allele frequency (MAF) of ≥0.02

10,700

LD filters with a correlation coefficient (r2) threshold of 0.2

10,624

HWE filters (p ≥ 0.0001)

10,624

Retained SNPs for further analysis

10,624