Deletion detection and functional annotation of chromosome 1 substitution strains from Chinese wild mice
10.3969/j.issn.1005-4847.2017.01.004
- VernacularTitle:中国野生小鼠来源1号染色体替换系缺失突变的发掘及功能注释
- Author:
Fuyi XU
;
Tianzhu CHAO
;
Shixian HU
;
Kai LI
;
Yuxun ZHOU
;
Liangliang ZHOU
;
Junhua XIAO
- Keywords:
Deletion detection;
Next-generation sequencing;
Function annotation;
PCSSs
- From:
Acta Laboratorium Animalis Scientia Sinica
2017;25(1):20-24
- CountryChina
- Language:Chinese
-
Abstract:
Objective Deletion detection and annotation of 18 lines from the population of specific chromosome 1 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. SpeedSeq software was used to detect the deletion after read alignment. Further annotation was obtained using SnpEff software. Results 13803 dele?tions were identified among the 18 lines, the length of deletion was ranged from 51bp 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 dele?tions. 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.
