DOI: 10.5061/dryad.6gc6h
title: Data from: Development of an Arabis alpina genomic contig sequence dataset and application to single nucleotide polymorphisms discovery

description: The alpine plant Arabis alpina is an emerging model in the ecological
 genomic field which is well-suited to identifying the genes involved in
 local adaptation in contrasted environmental conditions, a subject which
 remains poorly understood at molecular level. This paper presents the
 assembly of a pool of A. alpina genomic fragments using Next Generation
 Sequencing technologies. These contigs cover 172 Mb of the A. alpina
 genome (i.e. 50% of the genome) and were shown to contain sequences giving
 positive hits against 96% of the 458 CEGMA core genes (Core Eukaryotic
 Genes Mapping Approach), a set of highly conserved eukaryotic genes.
 Regions presenting high nucleic sequence identity with 77% of the close
 relative Arabidopsis thaliana's genes were found, with an unbiased
 distribution across the different functional categories of A. thaliana
 genes. This new resource was tested using a resequencing assay to identify
 polymorphic sites. Sixteen samples were successfully analyzed and 127,041
 Single Nucleotide Polymorphisms identified. This contig dataset will
 contribute to improving understanding of the ecology of Arabis alpina,
 thus constituting an important resource for future ecological genomic
 studies.
description: variant pileup for
 sample 2 reads mappingPaired end reads from
 sample 2 genomic sequencing were mapped on Arabis alpina contigs with BWA.
 Variant pileup was obtanied with samtools from bam
 file.sample2_pileup_var.txt.bz2variant pileup for sample 1 reads mappingPaired end reads from sample 1 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtained with samtools from bam file.sample1_pileup_var.txt.bz2variant pileup for sample 3 reads mappingPaired end reads from sample 3 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.sample3_pileup_var.txt.bz2variant pileup for sample 4 reads mappingPaired end reads from sample 4 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.sample4_pileup_var.txt.bz2variant pileup for sample 5 reads mappingPaired end reads from sample 5 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.sample5_pileup_var.txt.bz2variant pileup for sample 6 reads mappingPaired end reads from sample 6 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.sample6_pileup_var.txt.bz2variant pileup for sample 7 reads mappingPaired end reads from sample 7 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.sample7_pileup_var.txt.bz2variant pileup for sample 8 reads mappingPaired end reads from sample 8 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.sample8_pileup_var.txt.bz2variant pileup for sample 9 reads mappingPaired end reads from sample 9 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.sample9_pileup_var.txt.bz2variant pileup for sample 10 reads mappingPaired end reads from sample 10 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.sample10_pileup_var.txt.bz2variant pileup for sample 11 reads mappingPaired end reads from sample 11 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.sample11_pileup_var.txt.bz2variant pileup for sample 12 reads mappingPaired end reads from sample 12 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.sample12_pileup_var.txt.bz2variant pileup for sample 13 reads mappingPaired end reads from sample 13 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.sample13_pileup_var.txt.bz2variant pileup for sample 14 reads mappingPaired end reads from sample 14 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.sample14_pileup_var.txt.bz2variant pileup for sample 15 reads mappingPaired end reads from sample 15 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.sample15_pileup_var.txt.bz2variant pileup for sample 16 reads mappingPaired end reads from sample 16 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.sample16_pileup_var.txt.bz2arabis alpina filtered snp tableA summary of the filtered 127041 SNPs.The file provide : the contig name, the position on the contig, the reference base, the variant base, the global coverage, the average coverage, the phred mapping qualitysnp_table.txt.bz2