# GC content track

**TL;DR:** A GC content track plots the base composition of the reference genome
itself, with no data file required, sliding a window along the assembly's
sequence and drawing the result as a quantitative (wiggle) track. GC-rich and
GC-poor regions and isochores read off that profile. Switch the same track to GC
skew instead and its sign flips at a bacterial replication origin.

## Launching a GC content track from the sequence

Because the signal is derived from the reference sequence, you launch the track
straight off the reference sequence track:

- From the track selector, open the track menu (vertical "...") on the reference
  sequence track and choose **Add GC content track**.
- From an open sequence track, the sequence display's track menu has the same
  **Add GC content track** item.

Either route creates a `GCContentTrack` that wraps the assembly's existing
sequence adapter in a `GCContentAdapter`, so it works for any assembly, whether
its sequence is a 2bit, indexed FASTA, or bgzip-indexed FASTA. No new data is
fetched beyond the sequence the browser already reads.

<Figure caption="GC content (top, XY plot) and GC skew (bottom) computed on the fly across the whole H. pylori 26695 chromosome. The skew flips sign at the two points the Replication origin / terminus track marks." src="/img/gc_content.png" />

## GC content vs GC skew

The track menu's **GC skew** checkbox toggles between the two calculations (the
adapter's initial mode is the
[`gcMode`](https://jbrowse.org/jb2-staging/docs/config/gccontentadapter/#slot-gcmode) slot):

- GC content is the fraction of G+C bases in each window, a value between 0 and
  1. High values mark GC-rich regions.
- GC skew is `(G − C) / (G + C)`, which measures the strand imbalance between G
  and C. It swings positive and negative around zero, and in many bacterial
  genomes the sign flips at the replication origin and terminus.

## Adjusting the window

The track menu's **GC parameters** submenu has two sliders for the
sliding-window settings, each with a reset button:

- Window size is how many bases each point averages over. Larger windows smooth
  the signal and suppress local noise; smaller windows resolve finer structure.
- Step size is the distance between successive windows. Making the step smaller
  than the window size produces _overlapping_ windows, which gives a smoother,
  more finely-sampled curve (at the cost of more points to compute).

## Display options

The GC content track is a quantitative (wiggle) track under the hood, so it
inherits the full set of
[quantitative track](https://jbrowse.org/jb2-staging/docs/user_guides/quantitative_track) display options from
the same track menu: XY plot / line / density / scatter rendering, linear vs log
scale, autoscale modes, and manual min/max.

## See also

- [](https://jbrowse.org/jb2-staging/docs/user_guides/quantitative_track)
- [](https://jbrowse.org/jb2-staging/docs/user_guides/sequence_track)
- [GCContentAdapter configuration](https://jbrowse.org/jb2-staging/docs/config/gccontentadapter)