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. Author manuscript; available in PMC: 2011 Dec 1.
Published in final edited form as: Curr Protoc Bioinformatics. 2010 Dec;CHAPTER:Unit–11.7. doi: 10.1002/0471250953.bi1107s32

Figure 11.7.2.

Figure 11.7.2

Sample Bowtie session when SAM output mode is enabled. The last few lines are written to the “standard error” file handle and convey summary information about the run and are not part of the SAM format. The first few lines beginning with “@” are the SAM header. The remaining lines are alignments.