中文摘要：

[目的]鉴定B6-Chr1^LY和B6-Chr1^SJ小鼠品系1号染色体上的遗传变异。[方法]采用Illumina测序平台获得B6-Chr1^LY和B6-Chr1^SJ品系的全基因组序列并比对到参考基因组。利用Samtools/Bcftools以及speedseq软件鉴定单核苷酸多态性（single nucleotide polymorphism,SNP）、插入缺失（indel）和结构变异,并对其进行功能注释。[结果]两个品系共鉴定380万个SNPs、55万个indels、10 123个大片段缺失、152个重复和87个倒位。二者共享1 642 629 SNPs和190 248个indels;近16.1%SNPs和20.7%indels未在小鼠基因组计划和db SNP142数据集中报道。大片段缺失长度在51~70 kb之间,〈2 kb的占总数的76%。功能注释发现上百个蛋白编码基因含有非同义突变、移码突变、编码序列缺失等功能性变异。[结论]B6-Chr1^LY和B6-Chr1^SJ小鼠1号染色体上含有丰富的遗传变异信息,可为后续利用这两个品系的遗传学研究奠定基础。

英文摘要：

[ Objective] Detection and annotation of genetic variation of B6 -Chr1^LV and B6 -Chr1^SJ mouse strains from whole genome resequencing data. [ Methods ] B6 - Chr1^LY and B6 - Chr1^SJ whole genome resequencing were performed by Illumina X - Ten platform. Samtools/Bcftools and speedseq softwares were used to detect SNPs,indels and structure variation after reads a- lignment. Further annotation were obtained by variant effect predictor software from Ensembl. [ Results] A total of 38 million single nucleotide polymorphism（SNPs）,5.5 million indels, 10 123 deletions, 152 duplications, and 87 inversions were detec- ted. Among them,1 642 629 SNPs and 190 248 indels were found in both strains. There were 377 479 novel SNPs and 73 671 novel indels when compared with mouse genome project and dbSNP142 data sets. We also found that the length of deletion was ranged from 51 bp to 70 kb, and nearly 76% was less than 2 kb. Through functional annotation, hundreds of protein coding genes were identified with missense variants ,frameshift or coding sequence variants, etc. [ Conclusion] The chromosome 1 of B6 - Chr1^LY and B6 - Chr1^SJ harbored abundant genetic variations which can be used to guiding further genetic studies.