中文摘要：

目的基于野生小家鼠来源1号染色体替换系群体（population of specific chromosome 1 substitution strains,PCSSs）中18个品系的全基因组重测序结果,鉴定1号染色体上的缺失突变并对其进行功能注释。方法采用Illumina二代测序平台获取18个品系的全基因组序列信息,通过Speed Seq软件鉴定缺失突变,进一步利用Snp Eff软件完成功能注释。结果在18个品系的1号染色体上共检测到13 803个缺失突变。缺失长度从51 bp到70 kb不等,其中长度〈500 bp的缺失突变约占总数的50%。多数缺失突变位于内含子区（50.361%）和基因间隔区（28.745%）。发现31个蛋白编码基因含有功能性缺失,其中有3个基因和人类疾病相关,7个基因参与了11条KEGG通路。结论 PCSSs的1号染色体上含有丰富的缺失突变,是在研究复杂性状的重要遗传标记。

英文摘要：

Objective Deletion detection and annotation of 18 lines from the population of specific chromosome1 substitution strains（ PCSSs） derived from Chinese wild mice based on whole genome re-sequencing data. Methods Whole genome re-sequencing of the 18 lines were performed on the Illumina Hiseq platform. Speed Seq software was used to detect the deletion after read alignment. Further annotation was obtained using Snp Eff software. Results 13 803 deletions were identified among the 18 lines,the length of deletion was ranged from 51 bp to 70 kb,among them nearly 50%were less than 500 bp. Through functional annotation,we found most of the variants were located in intronic（ 50. 361%）and intergenic（ 28. 745%） regions. However,we also identified 31 protein coding genes harboring loss-of-function deletions. Among them,3 genes were associated with human diseases,7 genes were participated in 11 KEGG pathways.Conclusion The chromosome 1 of PCSSs harbors abundant deletion mutations which can be used as genetic markers in genetic studies.