When I use samtools' mpileup and vcfutils.pl to generate consensus sequences, the resulted fasta files contained lowercases, uppercases and "n".
After checking discussions in the board, I realized that vcfutils.pl does not put bases, which are out of the range of coverage and consensus quality I set, into "n", but puts them into lowercases.
Then I am confused what does the "n" really mean in the consensus? Does it mean there is no read mapped to that base at all?
One explanation I found in the board said: the only way an N gets put in is if the FQ is < 0 (which happens when your SNP is mixed), and there's no single letter code for that mix. But it is still not very clear to me.
Does anyone have a simpler explanation for the "n"?
Thank you in advance.
After checking discussions in the board, I realized that vcfutils.pl does not put bases, which are out of the range of coverage and consensus quality I set, into "n", but puts them into lowercases.
Then I am confused what does the "n" really mean in the consensus? Does it mean there is no read mapped to that base at all?
One explanation I found in the board said: the only way an N gets put in is if the FQ is < 0 (which happens when your SNP is mixed), and there's no single letter code for that mix. But it is still not very clear to me.
Does anyone have a simpler explanation for the "n"?
Thank you in advance.