I am pretty new to bioinformatics (so please go easy on me) and am trying to use Array Studios and IGV for some analysis. I have DNAseq data in the form of FASTQ, BAM and VCF files. Previously, I used Array Studios to view mutations from the VCF file using the Annotate Variants functions. This gave me a lot of good insight into mutations present in my DNA sample when compared to the reference genome. But recently I have wanted to look more closely into the actual sequences of my DNA sample, so I started using IGV to view the reads from the BAM files.

I quickly started to notice some discrepancies and I don't know if there is actually an issue or if it is due to a lack of understanding on my part. For example, in Array Studios say there is a mutation listed at position 123,456,789 on chromosome X from C->G. So I go to view that location in IGV and don't see a mutation; all of the aligned reads have a C in that position just like the reference genome.

Am I misunderstanding something here? I just can't understand why there would be a difference. Any help would be greatly appreciated.