Data from: The standing pool of genomic structural variation in a natural population of Mimulus guttatus

 

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Title SV_code_dryad
Downloaded 79 times
Description Python code library for identifying structural variation from paired-end illumina reads.
Download SV_code_dryad.zip (23.67 Kb)
Download README.txt (2.529 Kb)
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Title Deletion_Calls
Downloaded 61 times
Description Spreadsheet containing genomic deletion calls for all deletion alleles. Columns include: include accession and chromosomal location information, estimated deletion size (size), count of supporting illumina reads (num_reads), deletion allele includes ref. genome (contains_IM62), sequence read coverage in deleted interval (cov), "N" bases in deleted interval in ref. genome (prop_Ns). Annotation of gene and Transposable element hits (gene_hits and TE_hits; includes annoation and proportion deleted in parenthesis).
Download Deletion_Calls.xlsx (1.339 Mb)
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Title SNP.data.Supp.Table.txt
Downloaded 25 times
Description All SNPs collected from 12 Mimulus accessions. Columns listed include SNP position (scaffold and base position (pos)), SNP type (if coding, synonymous or nonsynonymous), and allele state for all 12 accessions. Missing data represented by a hyphen.
Download SNP.data.Supp.Table.txt.bz2 (7.309 Mb)
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Title SV.read.data.Supp.Table.txt
Downloaded 28 times
Description Read meta-data for all illumina reads implicated in a structural variant. Including read name, accession (line), structural variant category (kind), re-alignment status with Novoalign (reject_by_Novoalign), cluster formation status (failed_to_form_cluster), cluster ID (cluster), status of ref. genome line in cluster (cluster_includes_ref_line), status of cluster cov or alignment quality QC (failed_cov_or_abnormally_mapped_QC).
Download SV.read.data.Supp.Table.txt.bz2 (7.797 Mb)
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When using this data, please cite the original publication:

Flagel LE, Willis JH, Vision TJ (2013) The standing pool of genomic structural variation in a natural population of Mimulus guttatus. Genome Biology and Evolution 6(1): 53-64. http://dx.doi.org/10.1093/gbe/evt199

Additionally, please cite the Dryad data package:

Flagel LE, Willis JH, Vision TJ (2013) Data from: The standing pool of genomic structural variation in a natural population of Mimulus guttatus. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.41dq8
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