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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?).

My read headers from the given transcript are:

@Chr1:3631-5899W:AT1G01010.1:2:1688:10:276/1
@Chr1:3631-5899W:AT1G01010.1:2:1688:10:276/2
@Chr1:3631-5899W:AT1G01010.1:3:1688:1134:1342/1
@Chr1:3631-5899W:AT1G01010.1:3:1688:1134:1342/2
@Chr1:3631-5899W:AT1G01010.1:4:1688:886:1144/1
@Chr1:3631-5899W:AT1G01010.1:4:1688:886:1144/2
@Chr1:3631-5899W:AT1G01010.1:5:1688:1340:1686/1
@Chr1:3631-5899W:AT1G01010.1:5:1688:1340:1686/2

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.