Data from: Development of an Arabis alpina genomic contig sequence dataset and application to single nucleotide polymorphisms discovery

Lobreaux S, Manel S, Melo de Lima C

Date Published: October 14, 2013

DOI: http://dx.doi.org/10.5061/dryad.6gc6h

 

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Title variant pileup for sample 2 reads mapping
Downloaded 13 times
Description Paired end reads from sample 2 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.
Download sample2_pileup_var.txt.bz2 (50.27 Mb)
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Title variant pileup for sample 1 reads mapping
Downloaded 11 times
Description Paired end reads from sample 1 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtained with samtools from bam file.
Download sample1_pileup_var.txt.bz2 (29.09 Mb)
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Title variant pileup for sample 3 reads mapping
Downloaded 9 times
Description Paired end reads from sample 3 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.
Download sample3_pileup_var.txt.bz2 (28.31 Mb)
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Title variant pileup for sample 4 reads mapping
Downloaded 11 times
Description Paired end reads from sample 4 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.
Download sample4_pileup_var.txt.bz2 (62.52 Mb)
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Title variant pileup for sample 5 reads mapping
Downloaded 8 times
Description Paired end reads from sample 5 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.
Download sample5_pileup_var.txt.bz2 (26.37 Mb)
Details View File Details
Title variant pileup for sample 6 reads mapping
Downloaded 8 times
Description Paired end reads from sample 6 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.
Download sample6_pileup_var.txt.bz2 (44.33 Mb)
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Title variant pileup for sample 7 reads mapping
Downloaded 7 times
Description Paired end reads from sample 7 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.
Download sample7_pileup_var.txt.bz2 (43.62 Mb)
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Title variant pileup for sample 8 reads mapping
Downloaded 3 times
Description Paired end reads from sample 8 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.
Download sample8_pileup_var.txt.bz2 (54.15 Mb)
Details View File Details
Title variant pileup for sample 9 reads mapping
Downloaded 5 times
Description Paired end reads from sample 9 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.
Download sample9_pileup_var.txt.bz2 (44.16 Mb)
Details View File Details
Title variant pileup for sample 10 reads mapping
Downloaded 3 times
Description Paired end reads from sample 10 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.
Download sample10_pileup_var.txt.bz2 (27.94 Mb)
Details View File Details
Title variant pileup for sample 11 reads mapping
Downloaded 6 times
Description Paired end reads from sample 11 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.
Download sample11_pileup_var.txt.bz2 (26.72 Mb)
Details View File Details
Title variant pileup for sample 12 reads mapping
Downloaded 7 times
Description Paired end reads from sample 12 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.
Download sample12_pileup_var.txt.bz2 (40.34 Mb)
Details View File Details
Title variant pileup for sample 13 reads mapping
Downloaded 6 times
Description Paired end reads from sample 13 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.
Download sample13_pileup_var.txt.bz2 (44.37 Mb)
Details View File Details
Title variant pileup for sample 14 reads mapping
Downloaded 6 times
Description Paired end reads from sample 14 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.
Download sample14_pileup_var.txt.bz2 (30.36 Mb)
Details View File Details
Title variant pileup for sample 15 reads mapping
Downloaded 7 times
Description Paired end reads from sample 15 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.
Download sample15_pileup_var.txt.bz2 (34.82 Mb)
Details View File Details
Title variant pileup for sample 16 reads mapping
Downloaded 7 times
Description Paired end reads from sample 16 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.
Download sample16_pileup_var.txt.bz2 (22.84 Mb)
Details View File Details
Title arabis alpina filtered snp table
Downloaded 8 times
Description A 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 quality
Download snp_table.txt.bz2 (779.6 Kb)
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When using this data, please cite the original publication:

Lobreaux S, Manel S, Melo de Lima C (2014) Development of an Arabis alpina genomic contig sequence dataset and application to single nucleotide polymorphisms discovery. Molecular Ecology Resources 14(2): 411-418. http://dx.doi.org/10.1111/1755-0998.12189

Additionally, please cite the Dryad data package:

Lobreaux S, Manel S, Melo de Lima C (2013) Data from: Development of an Arabis alpina genomic contig sequence dataset and application to single nucleotide polymorphisms discovery. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.6gc6h
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