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Is the CNQ value the Phred quality score or the confidence percentile?

Dear Genome STRiP users,

I completed the SVCNVDiscovery to all the samples in a single batch. Beside of the CN, I also got the CNQ for the CN of each sample. Based on "https://gatkforums.broadinstitute.org/gatk/discussion/23345/is-there-any-pre-copy-number-value-in-the-processing#latest", CNQ should be the Phred quality score, but my CNQ value looks like

sample 1 sample 2 sample 3 sample 4 sample 5
53.1 99 80.2 46 93.4

And they look like the confidence percentile, but I am not sure. May I have your help to explain these CNQ values? Thank you very much.

Best regards,


Best Answer


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