mpilup output quality
Hi All
I was look at the samtools mpileup output format and found something odd in the reported quality scores.
1 633887 G 28 >><<<<CAAA.AA.AAAcaAAAC.A..a E//E/E6i/EiEEEEEE//AEE//EEEA
In the line above, some calls get a (phred+33 I assume) quality i. As I understand pileup format description (http://samtools.sourceforge.net/pileup.shtml), this should be the mapping quality of the reads at that base. However, when I look at the mapped reads at that position in the .bam file (using samtools view), I find no i quality scores anywhere near those positions.
Hence the question: what quality scores are reported by samtools mpileup?
• 1,262 views
•
link
written
by
mluypaert •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
samtools mpileup on mitochondrial bam results in incorrect base quality scores
written by gmora •
-
Multiple N bases in RNAseq
written by garcesj •
-
Samtools mpileup quality scores all zero
written by fwuffy
-
Samtools Pileup Format
written by robles.daniela
-
Bam-Readcount And Quality Score Encoding
written by loeblabstuff •
-
Depth Of Coverage Reported By Igv And Samtools Do Not Agree
written by Anjan
-
Changing Quality Scores Within Bam Files
written by matted
-
Samtools Pileup Format
written by Joanne Lim •
-
Variant Call Format - Explanation Of Quality Scores?
written by Ian
-
What Is The Difference Between Samtools Mpileup And Pileup
written by Ian
