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 13 803 deletions 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 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.