Samtools Mpileup Output

Question

[Sam]

Hi,

I have looked all over the web and cannot seem to find what the are the definitions of behind the the <, >, and ~ symbols in mpileup output. For example:

chr6 31506624 T 78 >>><><,$cCccccccccCCcCCCCCCCccCcCCCcCccccCccCCCcCccccccccccCCCCcCCcCcCcCCcccC^~c^~C

I appreciate your help!

[Doctoroots]

since this is still unanswered, i would suggest mailing to samtools support : [e-mail] or samtools author (heng li)

Answer 1

[Nina]

The symbols "<" and ">" were added to column 5 a few releases ago. These symbols mean that this position is "covered" by a large gap (ie we're inside the "N" element in the cigar of this read). Note that reads that have a gap at this position still contribute to the total coverage reported in column 4.

For completeness I should also mention that "*" is very similar, but in this case it means the position is covered by a small gap (ie a D element in the cigar)

Also, as described in the link drio provided, "^" is always followed by another symbol. This indicates that we are at the start of a read. If you subtract 33 from the ascii value of the symbol that follows "^" it gives you the mapping quality of the read whose first base covers this position.

In a similar vein "$" means one of the reads covers this position with its last base.

In your example, if you ignore "$" and the two instances of "^~" you will find that you have 78 characters remaining in col 5, which matches the coverage depth reported in col 4.

I learned about this because for the analysis I do, we don't want gaps to contribute to the coverage depth. Here's part of an awk command that we use to adjust the coverage depth to exclude gaps

{l=$4; if($5~/>/ || $5~/</ || $5~/*/ ) {gsub(/\^./,"");l-=split($5,a,"<")-1;l-=split($5,a,">")-1;l-=split($5,a,"*")-1}

Answer 2

[Drio]

chromosome coordinate ref_value num_of_Reads_covering_position alleles_seen_at_that_position base_quality_per_each_base

Details here.

The ascii value of the characters (minus 33) gives you the base qualities.

[Sam]

Hi Drio, thanks for the response. Could you be more specific about the <, >, and ~ characters?

[Drio]

Edited my answer per your request. Please check the link again. The original link was incorrect. All the details are there.

[Rm]

Quality score encoding: http://en.wikipedia.org/wiki/FASTQ_format#Encoding