GBS data of seven Brassica cultivars from Pakistan
Data files
Apr 23, 2024 version files 100.24 KB
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bnapus_2024.vcf
99.61 KB
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README.md
635 B
Abstract
The genotyping-by-sequencing (GBS) data was generated on seven Brassica cultivars from Pakistan as a purpose of varietal registration. After strict quality-control, only 501 high-quality SNP markers were retained with 0% missing data. These marker sites can be used for varietal identification and diversity analysis.
https://doi.org/10.5061/dryad.15dv41p4g
The GBS data of seven Brassica cultivars from Pakistan including:
1) NIA-Canola-2023
2) Surhan
3) Super Canola
4) NIA Toria Gold
5) Rainbow
6) Super Raya
7) Toria Selection-A.
Description of the data and file structure
The data file consists of 501 SNPs in vcf format with SNP positions from reference genome of Brassica napus PRJEB5043.
Sharing/Access information
The data is only accessible from DryAd.
Code/Software
BWA-MEM
Samtools
GATK
GATK Haplotype Caller
The DNA was extracted using CTAB method, and the sequencing library was prepared following standard guidelines of two restriction enzymes based strategy. The sequencing libraries were sequenced on T7 MGI-Seq platform. The raw sequencing reads were aligned to the Reference genome sequence of Brassica napus, and the SNPs were called using GATK variant calling pipeline. The vcf file generated is being uploaded which include 501 SNPs with 100% data availability.