Samtools mpileup: read base column symbols

Question

[Marvin]

I have checked the documenation here: http://samtools.sourceforge.net/pileup.shtml

Here is an output of column 5 (read base column):

samtools view -h bamfile.bam | samtools mpileup -B -f reference.fasta - | awk '{split($5,chars,""); for(i=1;i<=length($5);i++) print chars[i]}' | sort | uniq -c

12864 $
 527 *
 590 +
 236 -
59664 .
 634 1
 130 2
  53 3
   6 4
   3 5
   3 =
6205 A
4793 C
12863 F
4787 G
   7 M
  15 N
6692 T
12863 ^

The F occurs because the mapping quality is always F (thus I always see ^F where a read starts). I find it a little strange that the mapping quality is F for every read but that's actually not my question

[maybe it's because I chose -B ... need to continue reading what that BAQ computation is about ... I noticed that I lose information in the mpileup output if I don't use -B, that's why I use it]

I wonder about these symbols as they are not mentioned in the docs (at least with respect to column 5): * =

The = symbol occurs in only 1 line whereas the * symbols occur in multiple lines. The * symbols also occur in that line where = occurs, so here's an example showing both:

gi_identifier    378981    T    9    .$*+1=$*+1A.*+1=$*+1=$*+1M$*+1M$G+1T    ]]]JJJ]]J

What do these symbols mean?

[Istvan Albert]

Make sure to refer to the correct documentation: http://www.htslib.org/doc/samtools.html

[Marvin]

Oh and I am also wondering about that "+1M" ... ?

[dariober]

It does look weird to me as well. What aligner produced this bam file? Maybe post the sam header.

[Marvin]

The bam file in the command is the result of a Geneious function that lets you extract the SNP columns of an alignment/bam:

https://support.geneious.com/entries/22583802-Exporting-snp-data-for-phylogenetic-analysis

When I use the same command on the original bam file, I only get expected/documented symbols.

I guess I'll just exclude Geneious from the pipeline and identify the SNP columns myself.