Hi there!
Thanks for reaching out.
If your REF and ALT tracks appear visually similar despite high differences inraw_score it is likely that plot scaling is masking the difference. Try reducing the interval within plot_components to zoom in along the X axis for better visibility of differences.
It is also possible to have small change in raw_score between REF and ALT despite a high quantile_score. The quantile_score represents the percentile rank of the raw_score compared to a background distribution of common variants, standardizing the predicted impact across different scales rather than reflecting visual magnitude. So even if the change in raw_score is small in absolute numbers, it may be extremely unusual and significant compared to typical background noise and therefore yield a high absolute quantile_score.
Interpretation should primarily rely on the calculated variant scores rather than visual differences.
Kind regards,
Nicolene