Hi, I am running referencecn.mops on samples before and after a mutation accumulation experiment. I imagine this is quite similar to analyzing control vs tumour; the ancestral genotpye is the control, the mutation accumulation lines (propogated clonally) are like the 'tumour' samples.

This is some of the cnvr output I got (in csv):

"","seqnames","start","end","width","strand","A1","A2","A3","A4","A5","A6","A7"
"1","scaffold00002",1520001,1523000,3000,"*","CN2","CN1","CN2","CN2","CN2","CN2","CN2"
"2","scaffold00002",1775501,1780500,5000,"*","CN2","CN3","CN2","CN2","CN2","CN2","CN2"
"3","scaffold00002",1850001,1853500,3500,"*","CN2","CN3","CN2","CN2","CN2","CN2","CN2"
"4","scaffold00002",2178001,2182000,4000,"*","CN2","CN3","CN2","CN2","CN2","CN2","CN2"
"5","scaffold00003",228001,230000,2000,"*","CN2","CN2","CN2","CN2","CN2","CN2","CN2"
"6","scaffold00003",419001,422500,3500,"*","CN2","CN2","CN2","CN2","CN2","CN2","CN2"
"7","scaffold00003",889001,893000,4000,"*","CN2","CN2","CN2","CN2","CN2","CN2","CN2"

I would like to know what the CN of the control is since it is not displayed in the output of referencecn.mops. Is it simply CN2?

There are also some regions where all samples are CN2. In this case, are all samples the same CN as the control? If it is all the same, why is it displayed in the output at all? I was thinking that it would only output regions that differ in CN among samples.

Thank you in advance for you time.