What Does The N Stands For In Pileup File In Next Generation Sequencing?

According to wikipedia:

AGTCN denotes a base that did not match the reference on the forward strand agtcn denotes a base that did not match the reference on the reverse strand

What is the meaning of N here?

ngs pileup

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updated 13.0 years ago by venks

• written 13.0 years ago by kindlychung •

More generally, see IUPAC codes: http://www.bioinformatics.org/sms/iupac.html

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written 13.0 years ago by Alex Reynolds

2 answers

"N" would be an ambiguous base call in the read that is used as evidence during the pileup call.

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written 13.0 years ago by Matt Shirley

N is a no call/ambiguous call.. This happens when the sequencer cannot call a base in a read as either A/C/G/T.

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written 13.0 years ago by venks

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