Strange Patterns when graphing outputs

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Hello I am writing because I get a strange pattern when I visualize data output 
from Popoolation2 in R.  

I am comparing two populations.  I use the allelefreq_pwc and allelefreq_rc 
output files from the command perl <popoolation2-path>/snp-frequency-diff.pl to 
graph the major allele frequency in the first population against the allele 
frequency difference between the two populations..I would expect for this graph 
to look quite random however I see quite a few, and distinctive, vertical and 
horizontal lines.  This data set is not the only one where we have seen 
patterns of this nature.  What causes these patterns in the data.  I have 
attached the image of the graph

Best, 
Alyssa

Original issue reported on code.google.com by alyssa.w...@gmail.com on 10 Dec 2014 at 1:48

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Original comment by alyssa.w...@gmail.com on 10 Dec 2014 at 1:49

Attachments:

• all_dif1-2_maapop1.png

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wow weird, its probably something because of the digital nature of the data, so 
you have distinct coverage categories, ie 5, 6, 7,8 so the major allele 
frequency usually falls into a some distinct categories eg (1/5, or 3/17), to a 
lesser extent, but still, the allele frequency differences are also somewhat 
categorized.

Original comment by RoKof...@gmail.com on 24 Jan 2015 at 10:55