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Old 02-05-2012, 04:57 AM   #1
dkrtndhkd
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Default the meaning of sequence 'M','Y','K' in samtools?

I alignmed illumina pair end data using bwa and visualize it by samtools tview option.

the attached is screenshot of samtools tview window.

what's the meaning of letter 'M','Y','K'?
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Old 02-05-2012, 06:58 AM   #2
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I guess they are the standard 'ambiguity' codes representing SNPs:
http://www.chick.manchester.ac.uk/Si...PAC_codes.html
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Old 02-05-2012, 11:56 PM   #3
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Thank you!!
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