What exactly does the brown shading in a sequence represent?

asked 2017-12-16 15:06:12 -0700

Whit Athey gravatar image

updated 2017-12-17 08:14:16 -0700

What exactly does the brown shading in a sequence represent? The annotation just says "Reference Match", but most of the sequence where it matches the reference, the bases are colored as one of the four primary colors. Is the brown shaded base in the sample sequence or not?

Or, if the brown shading really does indicate a match to the reference sequence being used, why are not all of the matching bases colored brown. In my plot, only about 20% of bases are brown, even though all of them match. About 80% are getting the red-blue-yellow-green shading as though they were variants. How can I have only actual variants being colored different from brown?

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