Analyze covariate plots

Hi,

I have used AnalyzeCovariates to plot the before and after recalibration results. I noticed that the quality scores in insertion and deletion panel are quite high, is this normal? For covariates plot ( cycle and context), why are there positive and negative values for quality score accuracy (y-axis)? Is each point represent a base? Any documentation with detail explanations on how to interpret these plots?

Thanks.

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