This dataset contains 150,025 single nucleotide polymorphism (SNP) calls for 49 giant pandas. The SNPs are called from whole-genome shotgun sequencing data. The data is useful for studying the population genetics of pandas and are released in tandem with a paper describing conclusions drawn from this dataset.
This dataset includes SNPs in PLINK format, SNPs in GVCBLUP format and a supplemental table describing the genetic samples. After downloading resequencing reads for 49 pandas from the NCBI Sequence Read Archive, steps were taken to sort, filter and convert the data and prepare it for further analysis in PLINK and GVCBLUP. The files containing SNPs can be opened by text editors. During the study, these files were processed in PLINK (version 3.9) and GVCBLUP (version 1.90 beta). PLINK is available at http://pngu.mgh.harvard.edu/~purcell/plink/plink2.shtml. GVCBLUP is available at http://animalgene.umn.edu/gvcblub
This project was supported by project MN-16-043 of the Agricultural Experiment Station.
Garbe JR, Prakapenka D, Tan C, Da Y (2016) Genomic Inbreeding and Relatedness in Wild Panda Populations. PLoS ONE 11(8): e0160496.