Genome Browser Sequence Legend

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Overview

In OmicSoft Genome Browser, we use different legend to represent different variant for sequence alignment.

GB no legend.png

General legend

GB legend.png

  • *: Deletion.
  • A: The base 'A' is from a read which is aligned to minus strand.
  • A: The base 'A' is from a read which is aligned to plus strand.
  • A: The base 'A' whose quality is bad is from a read aligned to minus strand.
  • A: The base 'A' is an insertion.
  • A: The base 'A' is a variation.
  • C: The base 'C' which is soft clipped is from a read which is aligned to minus strand.
  • I: There is a long insertion here. Due to current space, we can not fully show the insertion sequence, the user need to use "shift"+selection to zoom in.
Tips.pngFor soft clip base, we only show that it is soft clipped and which strand it is aligned to, no further information are shown


Long insertion

For long insertion, when the space between two bases are too small to show all of them, we would show an insertion sign I just like the picture above. The use can use shift+select to further zoom in the area to see the full picture of the insertion.

GB long insertion.png