Questions about *alignments.txt.gz

[yifnzhao]

Hello,

I have two questions about *alignments.txt.gz:

1. As an example, I wonder how the following text should be interpreted. Does it mean there is a breakpoint between 1:1,363,501 and 1:30,180,408, or a pair of breakpoints flanking this region?

Global BP: : 1:1,363,501(-) to 1:30,180,408(+) SPAN 28816907 c_1_1347501_1372501_19C t000:13 ins_against_contig 0 del_against_contig 0 c_1_1347501_1372501_19C

2. What is the difference between Global BP and SECONDARY Global BP?

Thanks!