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The Extended Sam: The Symbols '=' And 'X' Vs 'M'

For visual inspection of alignments, it would be easier for tools like BWA to use the extended version of the format http://samtools.sourceforge.net/SAM1.pdf. The new version differentiates between matches and substitutions. So far for both matches and mismatches the same symbol 'M' is used. Any rationale behind this?

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updated by Istvan Albert Istvan Albert • written by ilonpilaaja • ilonpilaaja

Ah, excellent point. You can safely close this thread.

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written by ilonpilaaja • ilonpilaaja

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