Single Nucleotide Polymorphism Calls for 49 Giant Pandas

Garbe, John R
Da, Yang
2015-09-24
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Persistent link to this item

http://dx.doi.org/10.13020/D6MS32
 https://hdl.handle.net/11299/174479
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Collection period

9/24/15

Date completed

9/24/15

Date updated

Time period coverage

Geographic coverage

Source information

Panda sequence data from NCBI Sequence Read Archive (SRA053353), DNA Data Bank of Japan

Journal Title

Journal ISSN

Volume Title

Title

Single Nucleotide Polymorphism Calls for 49 Giant Pandas

Published Date

2015-09-24

Authors

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Author Contact

Garbe, John
jgarbe@umn.edu

Type

Dataset
Genomics Data

Abstract

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.

Description

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

Referenced by

Garbe JR, Prakapenka D, Tan C, Da Y (2016) Genomic Inbreeding and Relatedness in Wild Panda Populations. PLoS ONE 11(8): e0160496.
http://dx.doi.org/10.1371/journal.pone.0160496

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License

CC0 1.0 Universal Public Domain Dedication
 http://creativecommons.org/publicdomain/zero/1.0/

Publisher

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Data Repository for U of M (DRUM)

Funding information

This project was supported by project MN-16-043 of the Agricultural Experiment Station.

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Previously Published Citation

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Suggested citation

Garbe, John R; Da, Yang. (2015). Single Nucleotide Polymorphism Calls for 49 Giant Pandas. Retrieved from the Data Repository for the University of Minnesota (DRUM), http://dx.doi.org/10.13020/D6MS32.

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Description
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panda.zip
SNP data in Plink format and GVCBLUP format
(4.51 MB)

readme.txt
Description of data
(5.39 KB)

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