What is the meaning of suclonal information in the _ratio.txt file

[kmavrommatis]

Hi,
I am trying to understand what the columns: Subclone_CN and Subclone_Population mean in the file _ratio.txt.
I have the following examples from the _ratio.txt file

Chromosome	Start	Ratio	MedianRatio	CopyNumber	BAF	estimatedBAF	Genotype	UncertaintyOfGT	Gene	Subclone_CN	Subclone_Population
1	925888	0.76209	1.13487	3	-1	2	-	-1	1:925887-926116	3	0.773552
1	930204	1.52041	1.13487	3	-1	2	-	-1	1:930203-930407	3	0.773552
1	930953	0.895203	1.13487	3	-1	2	-	-1	1:930952-931127	3	0.773552

Based on this file the target region 925888.. should have CopyNumber 3 and a subclone with 0.77 CCF (Subclone_Population), correct?

but later in the same segment we have

Chromosome	Start	Ratio	MedianRatio	CopyNumber	BAF	estimatedBAF	Genotype	UncertaintyOfGT	Gene	Subclone_CN	Subclone_Population
1	945059	0.608181	0	0	-1	2	0	-1	1:945058-945177	3	0.773552
1	945609	0.791256	0	0	-1	2	0	-1	1:945608-945737	3	0.773552
1	946233	2.27771	0	0	1	2	0	-1	1:946232-946399	3	0.773552

where it appears that each of those target regions we have 0 copies, but a subclone with 3 copies and 0.77 CCF. How is this interpreted?

even more confusingly in another region of the genome

Chromosome	Start	Ratio	MedianRatio	CopyNumber	BAF	estimatedBAF	Genotype	UncertaintyOfGT	Gene	Subclone_CN	Subclone_Population
1	1353187	1.26031	0	0	-1	2	0	-1	1:1353186-1353370	6	0.951405
1	1353532	5.28891	0.808577	2	-1	0.5	AB	23.4944	1:1353531-1353701	6	0.951405
1	1353814	6.26684	0.808577	2	-1	0.5	AB	23.4944	1:1353813-1354327	6	0.951405

These target regions have 2 Copy numbers, but subclone with 6 copies at 0.95 CCF,

How can I interpret these results?
Notably the _CNVs file agrees with the CopyNumber column so in these cases I am not sure what we can make out of the Subclone relevant columns.

Thanks in advance for your kind help

[valeu]

Hi, the subclone detection is in Beta.. Unfortunately, I would not trust the results you show. (And generally, something seems to be wrong with the main calls of FREEC. What parameters do you use?)