samtools and IGV question

[fatakias]

I am new to samtools, IGV display and NGS in general. I have a two part question.

Part 1-
I would like to know how to interpret the output from "samtools mpileup" command. For example, in the attached txt file, column 5 has symbols like:
1- "^]," what does this denote?
2- "t" or "T" what is the difference between lower case and upper case?
3- What is "-C"?
4- why is "." or "," is used?
and so on.

Is there a comprehensive list where I can find all such information. Samtools FAQ has limited information. Any help is appreciated.
(a text file is attached herein that I am trying to interpret)

Part 2-
Is there a samtools script or easily available script that can parse the information and tell us the allele frequency / total number of A,T,G, C at each mapped position. An icon displays frequency when mouse is moved over mapped position. It would be helpful if I can extract the information from the command line .. what IGV tools function / application would be used for this.

Thanks in advance.

[Robby]

regarding part 1:

1. a symbol `^' marks the start of a read segment which is a contiguous subsequence on the read separated by `N/S/H' CIGAR operations. The ASCII of the character following `^' minus 33 gives the mapping quality.
2. T for a mismatch on the forward strand and t for a mismatch on the reverse strand
3. -C -> deletion of C
4. a dot stands for a match to the reference base on the forward strand, a comma for a match on the reverse strand

[swbarnes2]

This is the link to the page that explains pileup format:

http://samtools.sourceforge.net/pileup.shtml

You can get allele counts from the DP4 values in the vcf, which is simpler than parsing the pileup. And its a much smaller file, too.