Data from: Development of highly reliable in silico SNP resource and genotyping assay from exome capture and sequencing: an example from black spruce (Picea mariana)

Bousquet J, Pavy N, Gagnon F, Deschênes A, Boyle B, Beaulieu J

Date Published: September 17, 2015

DOI: http://dx.doi.org/10.5061/dryad.tr87v

 

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Title 29196_Reference_Picea_mariana_contigs
Downloaded 6 times
Description Reference Picea mariana contigs used for read mapping: contig number, length and nucleotide sequences.
Download 29196_Reference_Picea_mariana_contigs.txt (29.55 Mb)
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Title SNP_dataset_Varscan_software_part_01
Downloaded 5 times
Description SNP dataset from Varscan software, part 1: contig number, SNP position, reference and variant alleles and number of reads, variant frequency (VarFreq), Varscan P value, contig length, annotation with Picea glauca paired transcript and percent of homology.
Download SNP_dataset_Varscan_software_part_01.txt (11.03 Mb)
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Title SNP_dataset_Varscan_software_part_02
Downloaded 6 times
Description SNP dataset from Varscan software, part 2: contig number, SNP position, reference and variant alleles and number of reads, variant frequency (VarFreq), Varscan P value, contig length, annotation with Picea glauca paired transcript and percent of homology.
Download SNP_dataset_Varscan_software_part_02.txt (11.06 Mb)
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Title SNP_dataset_Varscan_software_part_03
Downloaded 3 times
Description SNP dataset from Varscan software, part 3: contig number, SNP position, reference and variant alleles and number of reads, variant frequency (VarFreq), Varscan P value, contig length, annotation with Picea glauca paired transcript and percent of homology.
Download SNP_dataset_Varscan_software_part_03.txt (11.08 Mb)
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Title SNP_dataset_Varscan_software_part_04
Downloaded 11 times
Description SNP dataset from Varscan software, part 4: contig number, SNP position, reference and variant alleles and number of reads, variant frequency (VarFreq), Varscan P value, contig length, annotation with Picea glauca paired transcript and percent of homology.
Download SNP_dataset_Varscan_software_part_04.txt (9.237 Mb)
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Title SNP_dataset_GS_reference_mapper_software
Downloaded 7 times
Description SNP dataset from GS reference mapper software: contig number, SNP position, reference and variant alleles, total depth and variant frequency (VarFreq).
Download SNP_dataset_GS_reference_mapper_software.txt (8.699 Mb)
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Title Genotype_PmGP1_Natural_Population
Downloaded 4 times
Description PmGP1 array genotyping results for all SNP accessions for trees from natural populations: genotypes for all SNPs of PmGP1 for trees from Picea mariana natural populations.
Download Genotype_PmGP1_Natural_Population.txt (4.855 Mb)
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When using this data, please cite the original publication:

Pavy N, Gagnon F, Deschênes A, Boyle B, Beaulieu J, Bousquet J (2015) Development of highly reliable in silico SNP resource and genotyping assay from exome capture and sequencing: an example from black spruce (Picea mariana). Molecular Ecology Resources 16(2): 588-598. http://dx.doi.org/10.1111/1755-0998.12468

Additionally, please cite the Dryad data package:

Bousquet J, Pavy N, Gagnon F, Deschênes A, Boyle B, Beaulieu J (2015) Data from: Development of highly reliable in silico SNP resource and genotyping assay from exome capture and sequencing: an example from black spruce (Picea mariana). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.tr87v
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