read order for IGV

[jianfen man]

Hi，I have sample with Tandem Repeat of DMD Exon51-55 by TRS . There are some Reverse Strand Reads conver the breakpoint. When I use IGV for check the breakpoint,I get 'read order' by IGV.I want to known the mean of ' read order  ', especially   for  Reverse Strand Reads.

Thank you.

[jianfen man]

And   I  want to know the diffence between Read  Order and Alignment order.

Thank you.  

[jianfen man]

Why are the order of the two segments same? 

[igv-help]

Read order is the order the segment appears in the read sequence.   This is independent of alignment.    Alignment order draws the segments in position order on the chromosome.   By convention position is the base of the + strand,  so whether the segments aligns to + or - strand does not affect its position.    In your example read and alignment order are the same.  This would not be the case for, example, and inversion.