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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.

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. Open this view in JBrowse ↗

The steps behind the figure above, run against your own data.

  1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses hpylori_26695.
  2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs features defined inline in the config.This figure uses “Replication origin / terminus (from GC skew)”.
  3. Drag the bar at the bottom edge of the track to resize it.“Replication origin / terminus (from GC skew)”.
  4. Track menu → Settings → colorA per-feature expression. The Color by... radios write a solid color, a per-attribute palette, and the strand preset only, so an expression of any other shape is authored on the track config.“Replication origin / terminus (from GC skew)”.
  5. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “GC content”.
  6. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “GC skew”.
  7. Type your region of interest into the location box and press Enter.This figure is at NC_018939.1.
  8. View menu → Bookmarks/highlights → Always show highlight chips (checked)Greyed out while highlights themselves are hidden — the chip is drawn on a highlight band. Leave it off and a band still reveals its chip while the pointer is over it.
  9. View menu → Zoom to region / use the location box, then add a highlightThis figure highlights 2 regions; highlights can also be set with the &highlight= URL parameter.

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session — swap in your own files afterwards.

Nothing happens? Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=https%3A%2F%2Fjbrowse.org%2Fdemos%2Fhpylori%2Fconfig.json&session=spec-%7B%22sessionTracks%22%3A%5B%7B%22type%22%3A%22GCContentTrack%22%2C%22trackId%22%3A%22gc_content_hpylori%22%2C%22name%22%3A%22GC+content%22%2C%22assemblyNames%22%3A%5B%22hpylori_26695%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22GCContentAdapter%22%2C%22sequenceAdapter%22%3A%7B%22type%22%3A%22IndexedFastaAdapter%22%2C%22fastaLocation%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fhpylori%2Fhpylori_26695.fa%22%2C%22locationType%22%3A%22UriLocation%22%7D%2C%22faiLocation%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fhpylori%2Fhpylori_26695.fa.fai%22%2C%22locationType%22%3A%22UriLocation%22%7D%7D%7D%2C%22displays%22%3A%5B%7B%22type%22%3A%22LinearGCContentTrackDisplay%22%2C%22displayId%22%3A%22gc_content_hpylori-display%22%2C%22gcMode%22%3A%22content%22%2C%22windowSize%22%3A2000%2C%22windowDelta%22%3A2000%7D%5D%7D%2C%7B%22type%22%3A%22GCContentTrack%22%2C%22trackId%22%3A%22gc_skew_hpylori%22%2C%22name%22%3A%22GC+skew%22%2C%22assemblyNames%22%3A%5B%22hpylori_26695%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22GCContentAdapter%22%2C%22sequenceAdapter%22%3A%7B%22type%22%3A%22IndexedFastaAdapter%22%2C%22fastaLocation%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fhpylori%2Fhpylori_26695.fa%22%2C%22locationType%22%3A%22UriLocation%22%7D%2C%22faiLocation%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fhpylori%2Fhpylori_26695.fa.fai%22%2C%22locationType%22%3A%22UriLocation%22%7D%7D%7D%2C%22displays%22%3A%5B%7B%22type%22%3A%22LinearGCContentTrackDisplay%22%2C%22displayId%22%3A%22gc_skew_hpylori-display%22%2C%22gcMode%22%3A%22skew%22%2C%22windowSize%22%3A20000%2C%22windowDelta%22%3A2000%2C%22height%22%3A160%7D%5D%7D%2C%7B%22type%22%3A%22FeatureTrack%22%2C%22trackId%22%3A%22hpylori_repl_origin%22%2C%22name%22%3A%22Replication+origin+%2F+terminus+%28from+GC+skew%29%22%2C%22assemblyNames%22%3A%5B%22hpylori_26695%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22FromConfigAdapter%22%2C%22features%22%3A%5B%7B%22refName%22%3A%22NC_018939.1%22%2C%22uniqueId%22%3A%22oriC%22%2C%22start%22%3A1598000%2C%22end%22%3A1618000%2C%22name%22%3A%22oriC+%28dnaA%29%22%2C%22color%22%3A%22%231e8484%22%7D%2C%7B%22refName%22%3A%22NC_018939.1%22%2C%22uniqueId%22%3A%22terminus%22%2C%22start%22%3A804000%2C%22end%22%3A824000%2C%22name%22%3A%22terminus%22%2C%22color%22%3A%22%23d62828%22%7D%5D%7D%7D%5D%2C%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22hpylori_26695%22%2C%22loc%22%3A%22NC_018939.1%22%2C%22showHighlightChips%22%3Atrue%2C%22highlight%22%3A%5B%7B%22refName%22%3A%22NC_018939.1%22%2C%22start%22%3A1598000%2C%22end%22%3A1618000%2C%22assemblyName%22%3A%22hpylori_26695%22%2C%22color%22%3A%22rgba%2830%2C132%2C132%2C0.14%29%22%7D%2C%7B%22refName%22%3A%22NC_018939.1%22%2C%22start%22%3A804000%2C%22end%22%3A824000%2C%22assemblyName%22%3A%22hpylori_26695%22%2C%22color%22%3A%22rgba%28214%2C40%2C40%2C0.12%29%22%7D%5D%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22hpylori_repl_origin%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22height%22%3A50%2C%22color%22%3A%22jexl%3Aget%28feature%2C%27color%27%29%22%7D%2C%22gc_content_hpylori%22%2C%22gc_skew_hpylori%22%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+gc_content

A figure adds its tracks to one session. The jbrowse CLI writes the same tracks into a config.json instead, where every session that opens it has them: add-track where flags cover the whole track, add-track-json where they do not.

jbrowse add-track-json '{
  "type": "GCContentTrack",
  "trackId": "gc_content_hpylori",
  "name": "GC content",
  "assemblyNames": [
    "hpylori_26695"
  ],
  "adapter": {
    "type": "GCContentAdapter",
    "sequenceAdapter": {
      "type": "IndexedFastaAdapter",
      "fastaLocation": {
        "uri": "https://jbrowse.org/demos/hpylori/hpylori_26695.fa",
        "locationType": "UriLocation"
      },
      "faiLocation": {
        "uri": "https://jbrowse.org/demos/hpylori/hpylori_26695.fa.fai",
        "locationType": "UriLocation"
      }
    }
  },
  "displays": [
    {
      "type": "LinearGCContentTrackDisplay",
      "displayId": "gc_content_hpylori-display",
      "gcMode": "content",
      "windowSize": 2000,
      "windowDelta": 2000
    }
  ]
}'

jbrowse add-track-json '{
  "type": "GCContentTrack",
  "trackId": "gc_skew_hpylori",
  "name": "GC skew",
  "assemblyNames": [
    "hpylori_26695"
  ],
  "adapter": {
    "type": "GCContentAdapter",
    "sequenceAdapter": {
      "type": "IndexedFastaAdapter",
      "fastaLocation": {
        "uri": "https://jbrowse.org/demos/hpylori/hpylori_26695.fa",
        "locationType": "UriLocation"
      },
      "faiLocation": {
        "uri": "https://jbrowse.org/demos/hpylori/hpylori_26695.fa.fai",
        "locationType": "UriLocation"
      }
    }
  },
  "displays": [
    {
      "type": "LinearGCContentTrackDisplay",
      "displayId": "gc_skew_hpylori-display",
      "gcMode": "skew",
      "windowSize": 20000,
      "windowDelta": 2000,
      "height": 160
    }
  ]
}'

jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "hpylori_repl_origin",
  "name": "Replication origin / terminus (from GC skew)",
  "assemblyNames": [
    "hpylori_26695"
  ],
  "adapter": {
    "type": "FromConfigAdapter",
    "features": [
      {
        "refName": "NC_018939.1",
        "uniqueId": "oriC",
        "start": 1598000,
        "end": 1618000,
        "name": "oriC (dnaA)",
        "color": "#1e8484"
      },
      {
        "refName": "NC_018939.1",
        "uniqueId": "terminus",
        "start": 804000,
        "end": 824000,
        "name": "terminus",
        "color": "#d62828"
      }
    ]
  }
}'

Run these where the config.json is, or add --out <dir>, and point each uri at your own file. The config needs hpylori_26695 already — jbrowse add-assembly adds yours. The location and the settings the steps carry are session state rather than track config — that half is the Session spec tab, or jbrowse set-default-session.

This session spec pastes after &session=spec- on any JBrowse Web instance.

{
  "sessionTracks": [
    {
      "type": "GCContentTrack",
      "trackId": "gc_content_hpylori",
      "name": "GC content",
      "assemblyNames": [
        "hpylori_26695"
      ],
      "adapter": {
        "type": "GCContentAdapter",
        "sequenceAdapter": {
          "type": "IndexedFastaAdapter",
          "fastaLocation": {
            "uri": "https://jbrowse.org/demos/hpylori/hpylori_26695.fa",
            "locationType": "UriLocation"
          },
          "faiLocation": {
            "uri": "https://jbrowse.org/demos/hpylori/hpylori_26695.fa.fai",
            "locationType": "UriLocation"
          }
        }
      },
      "displays": [
        {
          "type": "LinearGCContentTrackDisplay",
          "displayId": "gc_content_hpylori-display",
          "gcMode": "content",
          "windowSize": 2000,
          "windowDelta": 2000
        }
      ]
    },
    {
      "type": "GCContentTrack",
      "trackId": "gc_skew_hpylori",
      "name": "GC skew",
      "assemblyNames": [
        "hpylori_26695"
      ],
      "adapter": {
        "type": "GCContentAdapter",
        "sequenceAdapter": {
          "type": "IndexedFastaAdapter",
          "fastaLocation": {
            "uri": "https://jbrowse.org/demos/hpylori/hpylori_26695.fa",
            "locationType": "UriLocation"
          },
          "faiLocation": {
            "uri": "https://jbrowse.org/demos/hpylori/hpylori_26695.fa.fai",
            "locationType": "UriLocation"
          }
        }
      },
      "displays": [
        {
          "type": "LinearGCContentTrackDisplay",
          "displayId": "gc_skew_hpylori-display",
          "gcMode": "skew",
          "windowSize": 20000,
          "windowDelta": 2000,
          "height": 160
        }
      ]
    },
    {
      "type": "FeatureTrack",
      "trackId": "hpylori_repl_origin",
      "name": "Replication origin / terminus (from GC skew)",
      "assemblyNames": [
        "hpylori_26695"
      ],
      "adapter": {
        "type": "FromConfigAdapter",
        "features": [
          {
            "refName": "NC_018939.1",
            "uniqueId": "oriC",
            "start": 1598000,
            "end": 1618000,
            "name": "oriC (dnaA)",
            "color": "#1e8484"
          },
          {
            "refName": "NC_018939.1",
            "uniqueId": "terminus",
            "start": 804000,
            "end": 824000,
            "name": "terminus",
            "color": "#d62828"
          }
        ]
      }
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hpylori_26695",
      "loc": "NC_018939.1",
      "showHighlightChips": true,
      "highlight": [
        {
          "refName": "NC_018939.1",
          "start": 1598000,
          "end": 1618000,
          "assemblyName": "hpylori_26695",
          "color": "rgba(30,132,132,0.14)"
        },
        {
          "refName": "NC_018939.1",
          "start": 804000,
          "end": 824000,
          "assemblyName": "hpylori_26695",
          "color": "rgba(214,40,40,0.12)"
        }
      ],
      "tracks": [
        {
          "trackId": "hpylori_repl_origin",
          "type": "LinearBasicDisplay",
          "height": 50,
          "color": "jexl:get(feature,'color')"
        },
        "gc_content_hpylori",
        "gc_skew_hpylori"
      ]
    }
  ]
}

Loaded against config: https://jbrowse.org/demos/hpylori/config.json

The same view with jbrowse-anywidget. Point the adapter at your own file.

from jbrowse_anywidget import LinearGenomeView, make_assembly

view = LinearGenomeView(
    assembly=make_assembly("hpylori_26695", "https://your-server/your-genome.fa.gz"),
    location="NC_018939.1",
)

view.add_track({
    "type": "FeatureTrack",
    "trackId": "my_track_1",
    "name": "My track 1",
    "assemblyNames": ["hpylori_26695"],
    "adapter": {"type": "FromConfigAdapter", "uri": "https://your-server/your-file"},
})
view.add_track({
    "type": "GCContentTrack",
    "trackId": "my_track_2",
    "name": "My track 2",
    "assemblyNames": ["hpylori_26695"],
    "adapter": {"type": "GCContentAdapter", "uri": "https://your-server/your-file"},
})
view.add_track({
    "type": "GCContentTrack",
    "trackId": "my_track_3",
    "name": "My track 3",
    "assemblyNames": ["hpylori_26695"],
    "adapter": {"type": "GCContentAdapter", "uri": "https://your-server/your-file"},
})

view  # display the widget

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "sessionTracks": [
    {
      "type": "GCContentTrack",
      "trackId": "gc_content_hpylori",
      "name": "GC content",
      "assemblyNames": [
        "hpylori_26695"
      ],
      "adapter": {
        "type": "GCContentAdapter",
        "sequenceAdapter": {
          "type": "IndexedFastaAdapter",
          "fastaLocation": {
            "uri": "https://jbrowse.org/demos/hpylori/hpylori_26695.fa",
            "locationType": "UriLocation"
          },
          "faiLocation": {
            "uri": "https://jbrowse.org/demos/hpylori/hpylori_26695.fa.fai",
            "locationType": "UriLocation"
          }
        }
      },
      "displays": [
        {
          "type": "LinearGCContentTrackDisplay",
          "displayId": "gc_content_hpylori-display",
          "gcMode": "content",
          "windowSize": 2000,
          "windowDelta": 2000
        }
      ]
    },
    {
      "type": "GCContentTrack",
      "trackId": "gc_skew_hpylori",
      "name": "GC skew",
      "assemblyNames": [
        "hpylori_26695"
      ],
      "adapter": {
        "type": "GCContentAdapter",
        "sequenceAdapter": {
          "type": "IndexedFastaAdapter",
          "fastaLocation": {
            "uri": "https://jbrowse.org/demos/hpylori/hpylori_26695.fa",
            "locationType": "UriLocation"
          },
          "faiLocation": {
            "uri": "https://jbrowse.org/demos/hpylori/hpylori_26695.fa.fai",
            "locationType": "UriLocation"
          }
        }
      },
      "displays": [
        {
          "type": "LinearGCContentTrackDisplay",
          "displayId": "gc_skew_hpylori-display",
          "gcMode": "skew",
          "windowSize": 20000,
          "windowDelta": 2000,
          "height": 160
        }
      ]
    },
    {
      "type": "FeatureTrack",
      "trackId": "hpylori_repl_origin",
      "name": "Replication origin / terminus (from GC skew)",
      "assemblyNames": [
        "hpylori_26695"
      ],
      "adapter": {
        "type": "FromConfigAdapter",
        "features": [
          {
            "refName": "NC_018939.1",
            "uniqueId": "oriC",
            "start": 1598000,
            "end": 1618000,
            "name": "oriC (dnaA)",
            "color": "#1e8484"
          },
          {
            "refName": "NC_018939.1",
            "uniqueId": "terminus",
            "start": 804000,
            "end": 824000,
            "name": "terminus",
            "color": "#d62828"
          }
        ]
      }
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hpylori_26695",
      "loc": "NC_018939.1",
      "showHighlightChips": true,
      "highlight": [
        {
          "refName": "NC_018939.1",
          "start": 1598000,
          "end": 1618000,
          "assemblyName": "hpylori_26695",
          "color": "rgba(30,132,132,0.14)"
        },
        {
          "refName": "NC_018939.1",
          "start": 804000,
          "end": 824000,
          "assemblyName": "hpylori_26695",
          "color": "rgba(214,40,40,0.12)"
        }
      ],
      "tracks": [
        {
          "trackId": "hpylori_repl_origin",
          "type": "LinearBasicDisplay",
          "height": 50,
          "color": "jexl:get(feature,'color')"
        },
        "gc_content_hpylori",
        "gc_skew_hpylori"
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/hpylori/config.json \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

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 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 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