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Comment: Migrated to Confluence 5.3

Hello Michael,

Here is a modified extract from my *.pro file. Since my reference transcript length is 1688bp, and the covered fraction as shown, the actual covered length of the transcript comes to 588bp (am I right there?).

locustranscript_IDlengthexpressed fractionexpressed numbersequenced fractionsequenced numbercovered fraction


My read headers from the given transcript are:

Code Block


My questions are:


  • Are the coordinates 1-based or 0-based? Simply put, are the first fragment coordinates [10,276] or (10,276] in the first pair of reads?

  • What does the length 588bp refer to?


Thanks for your time and help.