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What Exactly is "Match Depth"

asked 2016-05-28 18:57:39 -0600

At some locations the consensus base call in the "Read Depth" track is colored brown (it seems to match the reference). The corresponding strands in the "Pile Up" track do not show a base call. In the "Read Depth" track, a mouse-over of the base shows (for example) "Read Depth 14". When the base in the "Read Depth" track is colored one of the four colors, a mouse-over shows something like "C Depth 15". What is the difference between "Match Depth" and normal read depth? Is the distinction between the colored or brown locations something assessed and added by the browser or is it something from the BAM file? Why would the property causing the brown coloring be uniform across all the strand reads?

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answered 2016-05-30 03:57:14 -0600

Never mind--I have found my problem--I wasn't using the appropriate reference--the "Match" is just the normal indication and is colored brown. The coloration is just for variants.

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answered 2016-05-28 18:59:54 -0600

Correction: where I wrote "Read Depth 14" in the third sentence, it should have been "Match Depth 14".

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Asked: 2016-05-28 18:57:39 -0600

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Last updated: May 30 '16