Detection and characterization of small insertions and deletions in modern layer chicken genomes

The present project reports on the detection and characterisation of high quality InDels (Small insertions and deletions) from the whole-genome analysis of several modern layer chicken lines from diverse breeds. The data was generated by Illumina sequencing of 163 chickens originating from 11 commercial and 5 experimental layer lines. The InDel calling was performed with SAMtools and Dindel package followed by stringent filtration. This study provides an in-depth characterisation of the InDels by adopting different approaches such as annotation against known genes, prediction of deleteriousness of nonframeshift variants, etc.