Data from: "Discovery and characterization of 80 SNPs and 1,624 SSRs in the transcriptome of Atlantic mackerel (Scomber scombrus, L)" in Genomic Resources Notes Accepted 1 June 2015 to 31 July 2015

Montes I, Langa J, Vilas C, Helyar SJ, Álvarez P, Conklin D, Estonba A

Date Published: August 17, 2015

DOI: http://dx.doi.org/10.5061/dryad.3rg62

 

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Title SSR and SNP markers discovered for Atlantic mackerel
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Description SSRs: The 1,624 SSR markers detected in the Atlantic mackerel transcriptome. SSR names follow the format Ssco_[A]-[B] where [A] indicates the transcriptome contig where the SSR was detected and [B] indicates the number of SSR in the contig. SNPs:. The 80 validated SNPs sequences and their descriptive statistics. For each marker following information is provided: NCBI Submitter SNP (ss) accession numbers, reference and alternative alleles, call rate (%), minor allele frequency (MAF), global (pooling the three sampling locations) expected heterozygosity (He), global and per location deviation (p-value) from the Hardy-Weinberg equilibrium (HWE), and flanking sequence. SNP names follow the format [A]_[B] where [A] indicates the contig number and [B] indicates the SNP position in that contig. Target SNP is encoded in the sequence as [REF/ALT] where REF indicates the reference allele ALT indicates the alternative allele. * corresponds to p-value < 0.0001. SIGN. means that at least 1 location is not in HWE for these markers. N.S. corresponds to not significant.
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Title Atlantic mackerel transcriptome sequence files (.sff)
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Title Atlantic mackerel genome sequence files (.fastq) for the 10 individuals analyzed
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Title Atlantic mackerel transcriptome assembly (.fasta)
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Title Atlantic mackerel T2T and G2T alignment files (.bam)
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Title Atlantic mackerel T2T and G2T variant files (.vcf)
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When using this data, please cite the original publication:

Genomic Resources Development Consortium, Álvarez P, Arthofer W, Coelho MM, Conklin D, Estonba A, Grosso AR, Helyar SJ, Langa J, Machado MP, Montes I, Pinho J, Rief A, Schartl M, Schlick-Steiner BC, Seeber J, Steiner FM, Vilas C (2015) Genomics Resources Notes accepted 1 June 2015 - 31 July 2015. Molecular Ecology 15(6): 1510–1512. http://dx.doi.org/10.1111/1755-0998.12454

Additionally, please cite the Dryad data package:

Montes I, Langa J, Vilas C, Helyar SJ, Álvarez P, Conklin D, Estonba A (2015) Data from: "Discovery and characterization of 80 SNPs and 1,624 SSRs in the transcriptome of Atlantic mackerel (Scomber scombrus, L)" in Genomic Resources Notes Accepted 1 June 2015 to 31 July 2015. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.3rg62
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