Samtool Pileup file

[wuhoucdc]

Hello All,

Have you seen a pileup file like this?
chr1 862 N G 4 0 3 1 ^$G 8
chr1 863 N C 4 0 3 1 C 8
chr1 864 N A 4 0 3 1 A 8
chr1 865 N A 4 0 3 1 A 9
chr1 866 N G 4 0 3 1 G 8
chr1 867 N C 4 0 3 1 C /
chr1 868 N C 4 0 3 1 C 5
chr1 869 N T 4 0 3 1 T *
chr1 870 N A 8 0 4 2 A^&A 58
chr1 871 N C 8 0 4 2 CC 53

This is ten rows of my file, actually all the data in chr1 look like this.
I used $ samtools pileup -f chr1.fa -c sample.chr1.bam > sample.chr1.raw.txt.

Thank you very much!

Wu

[swbarnes2]

That looks about what you'd expect if that area of your reference has a sequence of n's (or, Samtools didn't figure out your reference file properly) which is covered by a single read.

The only surprising part is the last column. That should be one single letter Ascii letter per read crossing that point, and the ascii letter represents the quality score of that exact read letter. But the Ascii ranges usually used today, at least on Illumina instruments, start at @, which is after the numbers. So it's possible that some piece of software might not be scaling your fastq quality scores properly.