Matching bases highlighted in IGV

[tahamasoodi]

Hi,

Why does some of the bases that match with the reference genome are highlighted (shown) in Integrated genomics viewer even when the "Show all bases" option is off? What does these bases signify?

Thanks.

[tahamasoodi]

Any suggestions!

[sBeier]

http://www.broadinstitute.org/igv/AlignmentData
It says there:
At higher resolutions read bases that do not match the reference are color coded, and insertions and deletions relative to the reference become visible. By default, read bases that match are displayed in gray. To color code all bases, regardless of whether they are mismatched, right-click the track and select Show All Bases from the pop-up menu.

I guess what you look at is an alignment with mismatched bases?

[tahamasoodi]

I'm saying that the bases which match with the reference are also in some places shown when the Show All Bases option is off.

[sBeier]

Could you post a screenshot? Otherwise it is hard to guess.