MASPOT panel GBS genotype data - v6.1 reference

Genotype-by-sequencing data of the MASPOT panel clones (762 clones in total, 755 with phenotypes) generated by Illumina sequencing of leaf tissue cf. (Sverrisdottir et al., 2017). Biallelic variants have been called relative to the v6.1 Phureja double monoploid reference genome. The SNPs have been filtered to root mean square mapping quality of > 30, MAF > 1 %, missing data < 50 %, and minimum reading depth of 5x. This leaves 175435 variants. F1 sample names are in HEADER.SAMPLES, SNP identifyer and coordinates are in FILT3.KEY (both outlined in the new readme.txt. The genotypes are in the SNP_V1.0_DMv6.vcf.FILT3_FINAL.DISC.gz file. The snp_counts.txt is a file of the SNP counts in the full sets of filtration we have computed. For our purpose, we use only the discrete genotypes and the FILT3 filtration in version 1. This has the 175435 variants. The phased MASPOT parent genotypes are in the MASPOT_phased_genome_FILT3_modified_filtered.vcf.gz file. These are the genotype calls for the 18 MASPOT parents, phased to the long read sequencing files using WhatsHap. They are filtered to 1) SNPs passing the quality the FILT3 quality filters, 2) SNPs that are also called for the F1 panel, and 3) SNPs where all parents are phased. The latter, to allow imputation of all offspring. This leaves a subset of 112720 SNPs. Please see the readme.txt file for explanation of the content of each file. For our analysis, we are using the FILT3 filtration settings (outlined above) and discrete scale genotypes.本数据集为MASPOT群体克隆的基因型测序（Genotype-by-sequencing）数据，共计762个克隆，其中755个携带表型信息，通过Illumina对叶片组织进行测序获得，实验方法参照Sverrisdottir等（2017年）的研究。双等位变异基于v6.1版本的Phureja双单倍体参考基因组进行基因型调用。后续对单核苷酸多态性（Single Nucleotide Polymorphism, SNP）进行过滤，过滤标准为：均方根映射质量大于30、最小等位基因频率（Minor Allele Frequency, MAF）大于1%、缺失数据占比低于50%，且最低测序深度为5倍，最终保留175435个变异位点。 F1样本名称存储于HEADER.SAMPLES字段，SNP标识符与坐标信息存储于FILT3.KEY字段，二者的详细说明均见新增的readme.txt文件。基因型数据存放于SNP_V1.0_DMv6.vcf.FILT3_FINAL.DISC.gz压缩文件中。snp_counts.txt文件记录了我们通过全套过滤流程计算得到的SNP数量。本研究仅使用离散型基因型以及版本1的FILT3过滤集，该过滤集包含上述175435个变异位点。 已完成定相的MASPOT亲本基因型存储于MASPOT_phased_genome_FILT3_modified_filtered.vcf.gz压缩文件中。该文件包含18个MASPOT亲本的基因型调用结果，通过WhatsHap工具结合长读长测序文件完成定相。该数据集经过三重过滤：1）通过FILT3质量过滤的SNP；2）可在F1群体中被成功调用的SNP；3）所有亲本均完成定相的SNP。最后一项过滤旨在实现所有子代的基因型推断，最终保留112720个SNP位点。 各文件的详细内容说明请参阅readme.txt文件。 本研究的分析将采用上述FILT3过滤设置以及离散尺度基因型。