what does these mean?

[gigigou]

Recently I'm using BFAST to do some alignments.
In the output SAM file there are many columns. After reading the document of SAM, I still have a question about the CIGAR.
There are some alignments with CIGAR being "32M1D3M". In the document it says that "M: alignment match, D:deletion from the reference, I:insertion to the sequence". So what does the number before "MDI" mean? Does it mean the postion? If so, why does there be a 3M after 32M? Why does it not been presented in order, just like "1D3M32M"? Cause I notice there is one alignment wiht CUGAR beig "4M6I25M".
Could anyone help me?
Thanks a lot.

[alex_kur]

Number before symbol in CIGAR string means number of letters with this tag continiously from the start of the read. So, in your case, 32M1D3M signifies that from the start of the read you have 32 matched letters followed by one deletion which is followed by 3 matched letters else. For example:
AAT*AG -read with deletion
AATAAG -reference.
So, CIGAR will be 3M1D2M

[gigigou]

Number before symbol in CIGAR string means number of letters with this tag continiously from the start of the read. So, in your case, 32M1D3M signifies that from the start of the read you have 32 matched letters followed by one deletion which is followed by 3 matched letters else. For example:
AAT*AG -read with deletion
AATAAG -reference.
So, CIGAR will be 3M1D2M

Get it!
Thank you very much! Your words really help me a lot!

[gigigou]

Number before symbol in CIGAR string means number of letters with this tag continiously from the start of the read. So, in your case, 32M1D3M signifies that from the start of the read you have 32 matched letters followed by one deletion which is followed by 3 matched letters else. For example:
AAT*AG -read with deletion
AATAAG -reference.
So, CIGAR will be 3M1D2M

How do I get the mismatch information from the sam output?

[alex_kur]

generally you do not have to parse SAM manually. Use "samtools mpileup" output or special SNP-callers as "freebayes" or something else.