I've been analysing Bionano Genomics .bnx file format. The BNX File Format Specification Sheet contains only very brief description of the Quality Score values (QX11, QX12, etc.): as a label SNR or a label average intensity for a particular channel.
However, I used dataset bnx files available on Bionano website and i.a. I computed the ratio between QX11 and QX12 for several molecules from different files. I noticed that there are some cases when QX11/QX12 is almost constant within one molecule. In fact the difference between minimum and maximum values of that ratio for one molecule can be as low as e.g. 0.0002%, which seems to be only caused by the low precision of the numbers in the bnx file. On the other hand there can be differences of 30% (or even much more) for other molecules in the same file.
Does anyone know why the QX11/QX12 ratio happen to be so constant in some cases?
Can anyone advise me where I can find more details about the Quality Score values and how they are determined (so far I haven't found anything valuable neither within Bionano website nor anywhere else)?
Thank you in advance for any help.