Equal signs on reads

[fvigoder]

Hi,

I`m having an issue visualizing reads sequences in IGV.

I`m trying to see the sequence of reads but many are displaying = instead of the bases. 

What does the = means?

Is it an error from the alignment?

[James Robinson]

Its a convention allowed in the SAM/BAM specification,  I don't often see it used.   Here's what the spec document says

An `=' denotes the base is identical to the reference base.

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