Published December 6, 2021 | Version v1
Dataset Restricted

Dataset with SNP genotypes for local goat breeds of Mongolia (PLINK format)

Authors/Creators

  • 1. Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia; Institute for Information Transmission Problems, Russian Academy of Sciences, 127051 Moscow, Russia
  • 2. Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
  • 3. Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia; Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia

Description

SNP genotyping was performed with Goat 50K BeadChip (Illumina Inc., USA) containing ~60 000 SNP. Quality control was performed by setting a cutoff of 0.5 for the GenCall and GenTrain scores. SNP dataset was filtered to remove poorly genotyped individuals, loci genotyped in <90% of individuals and rare alleles using PLINK 1.9 (Chang et al. 2015) with geno 0.1 --mind 0.1 --maf 0.05 plink parameters. To ensure that our analysis would not be affected by the presence of SNP in strong linkage disequilibrium we also filtered data with --indep-pairwaise 50 5 0.2 PLINK filter. 

Notes

Funding: This work has been supported by the grants the Russian Science Foundation, RSF 19-76-20061.

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