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!
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https://en.wikipedia.org/wiki/Pileup_format
https://www.biostars.org/p/8371/
Which N's are you talking about? Please elaborate.
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
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.
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Did you type
?in the viewer?What does the star mean then ?