Mapping whole genome sequencing of several strains of organism A to gene X

Hi every one. I got stuck in my NGS project and was wondering if someone can advise me.

I have downloaded Illumina paired-end reads of the whole genome of several M. tuberculosis strains from ENA database. I have a gene of 1800bp length (gene X) from M. tuberculosis. I want to investigate the SNPs variation of gene X among different strains of M. tuberculosis.

After evaluating the read quality, and trimming the reads, is it ok to map illumina DNA-seq reads against one single gene? Does this make sense or i am missing some steps in my analysis!

According to the literature, all the reads are mapped against the whole genome (ref genome), and not a single gene while based on my project, I have to map the whole genome to a single gene! Any suggestion is greatly appreciated.

I think you can just try it. The only thing that comes to my mind is that you maybe need to filter out some clipped reads. A mapping tool can clip the outsides of the read to make it map better to the reference. I don’t think it will be that much of a problem but it is the one thing that comes to my mind. You can also download the whole reference genome and check if your gen X is present in there with blast. And map against that full reference genome.