samtools tview symbols

Question

[biolab]

Dear all,

I have a question related to samtools tview symbols, for examples, the dots, commas, upper case letters, lower case letters etc. Also, what do Ns mean? I tried to find a manual online, but have not got it yet. Would you please provide me some information for those symbols?

Thank you very much!

[Dan D]

Did you type ? in the viewer?

[RT]

What does the star mean then ?

Answer 1

[Ashutosh Pandey]

https://en.wikipedia.org/wiki/Pileup_format

https://www.biostars.org/p/8371/

Which N's are you talking about? Please elaborate.

[biolab]

Hi, Ashutosh, your comment is very helpful. Now I understand what's the meanings of dot, comma, etc. For the Ns, I mean those Ns in the reference sequence line, such as follows. THANKS!

71        81        91        101       111
GGATGTATGATGGCGATACCGATTGNNNNNNNNNNNNNNNNNNNNNN

[Dan D]

Most reference sequences, including the human hg19 reference, contain bands of N bases. The official IUPAC definition for N is "any base", but the majority of the occurrences I've seen are long stretches of N representing centromeres and telomeres.

[biolab]

Thank you Dan. Your comment is helpful for me to understand the tview output.