EPITREE project - WGS SNPs Oak (ICPSR doi:10.15454/W4XFPF)

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Document Description

Citation

Title:

EPITREE project - WGS SNPs Oak

Identification Number:

doi:10.15454/W4XFPF

Distributor:

Portail Data INRAE

Date of Distribution:

2020-07-13

Version:

1

Bibliographic Citation:

Lesur Kupin, Isabelle, 2020, "EPITREE project - WGS SNPs Oak", https://doi.org/10.15454/W4XFPF, Portail Data INRAE, V1

Study Description

Citation

Title:

EPITREE project - WGS SNPs Oak

Identification Number:

doi:10.15454/W4XFPF

Authoring Entity:

Lesur Kupin, Isabelle (INRA - Institut National de la Recherche Agronomique)

Distributor:

Portail Data INRAE

Access Authority:

Lesur Kupin, Isabelle

Depositor:

Lesur Kupin, Isabelle

Date of Deposit:

2020-07-13

Study Scope

Keywords:

Biodiversity and Ecology, Genetic Resource

Abstract:

In the EPITREE project (https://www6.inrae.fr/epitree-project/Le-projet-EPITREE) we aim at studying the distribution of methylation sites in 10 oak (Q. petraea) genomes. To do so, we had to discriminate between true C/T SNPs and C>T substitutions caused by bisulfite conversion which can lead to misidentified unmethylated Cs. Thus, we performed a global SNPs detection and considered three SNP calling algorithms: bcfTools , FreeBayes and GATK. In order to accuratly identify polymorphisms in these 10 genomes, we selected SNPs identified by the three calling algorithms. We ended up with 15,727,742 SNPs. These SNPs are placed on the 1408 oak scafflods.

Kind of Data:

Dataset

Methodology and Processing

Sources Statement

Data Access

Notes:

<img src="https://www.etalab.gouv.fr/wp-content/uploads/2011/10/licence-ouverte-open-licence.gif" alt="Licence Ouverte" height="100"><a href="https://www.etalab.gouv.fr/licence-ouverte-open-licence">Licence Ouverte / Open Licence Version 2.0</a> compatible CC BY

Other Study Description Materials

Other Study-Related Materials

Label:

all_SNPs_pos_all_indiv_oak_final.txt

Text:

Set of 15,727,742 SNPs identified in oak (WGS) within the EPITREE project.

Notes:

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