Inferring effective population size and divergence time in the Lithuanian population according to high-density genotyping data Manage Created on 20 Jan 2020 - 11:29 by Alina Urnikyte

he data set consisted of 295 samples from unrelated Lithuanian individuals who indicated at least three generations of Lithuanian nationality. The average age of participants was 53 years. The samples were collected randomly from six ethnolinguistic regions of Lithuania: three regions from Aukstaitija (western (n = 52), southern (n = 51), and eastern (n = 48)) and three groups of Zemaitija (northern (n = 61), western (n = 24), and southern (n = 59)) (Figure S1). All samples were genotyped at the Department of Human and Medical Genetics, Biomedical Science Institute, Faculty of Medicine, Vilnius University, Lithuania with the Illumina HumanOmniExpress-12 v1.1 array (Illumina, San Diego, CA, USA), which includes 719 665 SNPs genome-wide distributed. Genotyping data quality control was performed according to the standard recommendations by the manufacturer. Individuals and SNPs with > 10% missing data, and with minor allele frequency (MAF) < 0.01 were excluded. SNPs with deviations from Hardy–Weinberg equilibrium (P < 10–4) were eliminated from the study. After quality control 1 individual was excluded with more than 10% missing genotypes (MIND > 0.1) and 568,040 autosomal SNPs remained.