Samtools tview: mysterious KKKK within introns.

[valei]

Hi all,
I'm performing RNA-seq data analysis. I'm visualizing the alignments with samtools tview program , the attached figure shows a portion of my alignment. I cannot understand what mean the KKKKKK in the intron. Can someone help me?

[mbblack]

The IUPAC standard codes for ambiguity - K means (G or T).

see http://www.bioinformatics.org/sms/iupac.html

[valei]

many thanks mbblack,
in principle I thought the same thing. But in the portion where you can see the KKKK there is an intron and any of my reads map in these region. In this case the character K should mean something else. What? I don't know....

[valei]

Nobody answer me.....

[kristina.gagalova]

I have the same question. Is there anybody who solved this issue?