Functional annotation of SNPs and INDELs from 52 highly diverse accessions of the model allopolyploid plant Brassica napus.

This data resource contains the functional annotation of SNPs and INDELs for 52 Brassica napus lines. The analyzed sequence data was produced in the frame of
the PreBreed-Yield project and was published (Snowdon et al. 2015, DOI: 10.1016/j.tplants.2015.04.013). The complete whole-genome shotgun resequencing data is archived at the European Nucleotide
Archive (http://www.ebi.ac.uk/ena) under the project numbers PRJEB5974 and PRJEB6069. The discovery of INDELs is based on a gapped alignment that was constructed using Bowtie2. Subsequently the
discovery of INDELs was performed using SAMtools/BCFtools using a minimal base quality of ‘-Q 30’ and a minimal read alignment quality of ‘-q 20’. BCFtools (version 1.2) was applied to screen for
raw INDELs. A posterior filtering was performed subsequently using minimal (8) and maximal read depth (50), as well as a stringent IMF (0.9) and IDV (8) setting to identify high quality and
homozygous sites. In total we detected 633,844 insertions and 469,860 deletions in the range between -20 and 20 bp sequence length. The discovery of SNPs was performed utilizing an un-gapped
alignment that was constructed for each genotype individually using SOAP v2. SNP calling has been performed with multiple prediction methods using the tools FaSD, Freebayes and SAMtools. The
approach assigned an additional confidence value to the predicted variant position (VP) by using the variant caller count (VCC) measurement. This measurement indicates how many variant calling
methods predict a particular VP. All displayed VPs passed the following criteria: bi-allelic, SNP quality score >= 100, homozygous, read depth >= 4 and a VCC >= 2. This resource comprises
in total ~16.5 million VPs that correspond to ~4.3 million unique positions in the Brassica napus Darmor-bzh reference genome (v4.2). All SNPs and INDELs subsequently were processed by the tool
CooVar to construct a functional annotation using 101k predicted gene models of Brassica napus (Chalhoub et al. 2014, DOI: 10.1126/science.1253435).