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Old 04-09-2010, 02:27 AM   #1
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Location: Spain

Join Date: Jul 2009
Posts: 133
Default Help interpreting samtools tview

can anyone help me interpreting the alignment at the position shown in the attached image? I can guess that there is a deletion of two bases but the consensus sequence shows an AA and then follow bases identical to the reference? Why the blue color to those AA's? To me it is not very clear the interpretation of the color code. When I press "?" the final section of help from tview shows:

Underline: secondary or orphan ---what is this?
Blue: 0-9 --- 0-9 what? is it number of reads?

thanks for your help.

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File Type: jpg s_2.2probable_DELv2.jpg (6.0 KB, 226 views)
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