Question

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

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10.7 years ago

kindlychung ▴ 60

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 • 2.7k views

ADD COMMENT • link updated 10.7 years ago by venks ▴ 740 • written 10.7 years ago by kindlychung ▴ 60

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

ADD REPLY • link 10.7 years ago by Alex Reynolds 35k

score 2 · Answer 1 · 2013-07-23

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10.7 years ago

Matt Shirley 10k

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

ADD COMMENT • link 10.7 years ago by Matt Shirley 10k

score 0 · Answer 2 · 2013-07-23

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10.7 years ago

venks ▴ 740

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.

ADD COMMENT • link 10.7 years ago by venks ▴ 740