Barley exome VCF and chloroplast genomes

These datasets relate to the paper 'Genetic erosion in domesticated barley and a hypothesis of a North African centre of diversity' (Civan et al., in preparation). The whealbi VCF file is a general-purpose diversity matrix constructed from the exome data produced by the Whealbi consortium. Redundant accessions (above an empirical threshold of IBS >0.985) were removed. The FASTA file is a multiple sequence alignment (MSA) of chloroplast genomes reconstructed from various sequencing datasets by mapping to the Morex chloroplast genome EF115541 (ncbi) used as a reference. The MSA was visually checked for misaligned regions and corrected manually where necessary (except homopolymers and microsatellites). The second inverted repeat has been removed prior to read mapping. The data can be used for phylogeographic inference. Note of caution - the alignment region 35,650-42,725 bp spanning the genes atpA, rps14, psaB and psaA contains multiple ambiguities due to a paralogous copy from the mitochondrial genome interfering with the assembly, and should be avoided in sequence analyses.本数据集关联于论文《栽培大麦的遗传侵蚀与北非多样性中心假说》（Civan等，待刊）。其中Whealbi VCF（变异检测格式，Variant Call Format）文件是由Whealbi联盟产出的外显子组数据构建的通用型多样性矩阵，已移除同源一致性（Identity By State，简称IBS）阈值大于0.985的冗余种质。FASTA文件为叶绿体基因组的多序列比对（Multiple Sequence Alignment，简称MSA）结果，其数据通过以NCBI数据库收录的Morex叶绿体基因组EF115541为参照序列，在进行读段比对前先移除第二个反向重复序列，最终对各类测序数据集进行比对重构得到；该多序列比对已通过人工目视检查错配区域，并在必要时进行手动校正（均聚物与微卫星区域除外）。本数据集可用于系统地理学推断。重要提示：比对区域35650–42725 bp涵盖基因atpA、rps14、psaB与psaA，由于线粒体基因组的旁系同源拷贝干扰了组装过程，该区域存在多处序列歧义，因此在序列分析中应避免使用该区域。