I did a bacterial whole genome sequencing by illumina platform. The quality raw reads were subjected for de novo assembly by using CGE-Bacterial Analysis Pipeline and obtained 4.9 Mb size draft genome, which is closer to the expected genome size of the bacteria. I have subjected my assembled draft genome for various comparative genome analysis such as, genomic island prediction, pan-genome analysis etc., At some point of time, I have noticed that my assembled bacterial genome has
(0.001463 Mb out of 4.9 Mb). Is it negligible factor for further downstream analysis, if it not please let me know the possibilities to fix this issue.
Thank you in advance.