Would this level of base pair mismatch suggest the data is inaccurate?

Question

[Lou11]

On viewing a bam file there frequently appears to be a large amount of base-pair mismatch such as this. Should this data be disregarded or is it in any way possible for this to be accurate data?

[GenoMax]

Are you using the right reference (genome build/organism) to view the data in IGV? It is possible that your sample has several changes compared to the reference (windows above are 25kb).

[Lou11]

I believe it is the right reference. The alternative (hg19) gives a hugely worse-looking result.

[GenoMax]

If you did not create the BAM yourself, check the header of the BAM for clues to see what genome build was used. Generally the alignment command should give you an indication. Use something like.

samtools view -H your.bam | grep "CL"