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.
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.
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