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GC content track

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. That profile shows GC-rich and GC-poor regions and isochores directly. 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 track computes the signal from the reference sequence, launch it 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.

Add GC content track creates a GCContentTrack whose GCContentAdapter reads the sequence of the assembly it is shown against, so it works for any assembly, whether its sequence is a 2bit, indexed FASTA, or bgzip-indexed FASTA. The adapter fetches no new data beyond the sequence the browser already reads.

GC content (top) and GC skew (bottom) computed on the fly across the H. pylori chromosome.
Open in JBrowse Web ↗

Or rebuild it from your own data:

Quickest: open the view, then File → Open track... for your files.

From scratch:

  1. Open your genome: Open new genome in JBrowse Desktop, or jbrowse add-assembly for JBrowse Web.This figure uses GCF_000307795.1, loaded from a .2bit genome.
  2. Add your track: File → Open track..., or check it in the track selector. Needs features defined inline in the config.This figure uses “Replication origin / terminus (from GC skew)”.
    1. Track menu → Settings → colorA per-feature expression. The Color by radios write a solid color, a field's palette, and the strand colors only, so an expression is authored on the track config.
  3. Add the next track the same way.This figure uses “GC content”.
  4. Add the next track the same way.This figure uses “GC skew”.
  5. Go to your region in the location box.This figure is at NC_018939v1.
  6. 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.

Paste into a coding agent, with your goal on the first line.

My goal: [write yours, e.g. this view of my own files, or these track settings in my config.json]

Start from this JBrowse view.
- Config it loads: https://jbrowse.org/demos/hpylori/config.json
- Tracks:
  - Replication origin / terminus (from GC skew) (hpylori_repl_origin), FeatureTrack, features defined inline in the config, drawn as LinearBasicDisplay
  - GC content (gc_content_hpylori), GCContentTrack, drawn as LinearWiggleDisplay
  - GC skew (gc_skew_hpylori), GCContentTrack, drawn as LinearWiggleDisplay

Docs: https://jbrowse.org/jb2/docs/agents_authoring/ (writing a config), https://jbrowse.org/jb2/docs/agents/ (driving a running JBrowse). Use the jbrowse-authoring, jbrowse-hosted-data and jbrowse-capture skills if you have them. Check any config with `npx @jbrowse/cli validate`, then render it and look: a config that loads is not yet a track that drew.

The session spec that draws the view:
{
  "sessionTracks": [
    {
      "type": "GCContentTrack",
      "trackId": "gc_content_hpylori",
      "name": "GC content",
      "assemblyNames": [
        "GCF_000307795.1"
      ],
      "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"
          }
        },
        "op": "content",
        "window": 2000,
        "step": 2000
      }
    },
    {
      "type": "GCContentTrack",
      "trackId": "gc_skew_hpylori",
      "name": "GC skew",
      "assemblyNames": [
        "GCF_000307795.1"
      ],
      "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"
          }
        },
        "op": "skew",
        "window": 20000,
        "step": 2000
      },
      "displays": [
        {
          "type": "LinearWiggleDisplay",
          "displayId": "gc_skew_hpylori-LinearWiggleDisplay",
          "height": 160
        }
      ]
    },
    {
      "type": "FeatureTrack",
      "trackId": "hpylori_repl_origin",
      "name": "Replication origin / terminus (from GC skew)",
      "assemblyNames": [
        "GCF_000307795.1"
      ],
      "adapter": {
        "type": "FromConfigAdapter",
        "features": [
          {
            "refName": "NC_018939v1",
            "uniqueId": "oriC",
            "start": 1598000,
            "end": 1618000,
            "name": "oriC (dnaA)",
            "color": "#1e8484"
          },
          {
            "refName": "NC_018939v1",
            "uniqueId": "terminus",
            "start": 804000,
            "end": 824000,
            "name": "terminus",
            "color": "#d62828"
          }
        ]
      }
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "GCF_000307795.1",
      "loc": "NC_018939v1",
      "highlight": [
        {
          "refName": "NC_018939v1",
          "start": 1598000,
          "end": 1618000,
          "assemblyName": "GCF_000307795.1",
          "color": "rgba(30,132,132,0.14)"
        },
        {
          "refName": "NC_018939v1",
          "start": 804000,
          "end": 824000,
          "assemblyName": "GCF_000307795.1",
          "color": "rgba(214,40,40,0.12)"
        }
      ],
      "tracks": [
        {
          "trackId": "hpylori_repl_origin",
          "height": 50,
          "encoding": {
            "color": {
              "value": "jexl:get(feature,'color')"
            }
          }
        },
        "gc_content_hpylori",
        "gc_skew_hpylori"
      ]
    }
  ]
}
Redraw the figure headlessly
cat > session.json <<'JSON'
{
  "sessionTracks": [
    {
      "type": "GCContentTrack",
      "trackId": "gc_content_hpylori",
      "name": "GC content",
      "assemblyNames": [
        "GCF_000307795.1"
      ],
      "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"
          }
        },
        "op": "content",
        "window": 2000,
        "step": 2000
      }
    },
    {
      "type": "GCContentTrack",
      "trackId": "gc_skew_hpylori",
      "name": "GC skew",
      "assemblyNames": [
        "GCF_000307795.1"
      ],
      "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"
          }
        },
        "op": "skew",
        "window": 20000,
        "step": 2000
      },
      "displays": [
        {
          "type": "LinearWiggleDisplay",
          "displayId": "gc_skew_hpylori-LinearWiggleDisplay",
          "height": 160
        }
      ]
    },
    {
      "type": "FeatureTrack",
      "trackId": "hpylori_repl_origin",
      "name": "Replication origin / terminus (from GC skew)",
      "assemblyNames": [
        "GCF_000307795.1"
      ],
      "adapter": {
        "type": "FromConfigAdapter",
        "features": [
          {
            "refName": "NC_018939v1",
            "uniqueId": "oriC",
            "start": 1598000,
            "end": 1618000,
            "name": "oriC (dnaA)",
            "color": "#1e8484"
          },
          {
            "refName": "NC_018939v1",
            "uniqueId": "terminus",
            "start": 804000,
            "end": 824000,
            "name": "terminus",
            "color": "#d62828"
          }
        ]
      }
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "GCF_000307795.1",
      "loc": "NC_018939v1",
      "highlight": [
        {
          "refName": "NC_018939v1",
          "start": 1598000,
          "end": 1618000,
          "assemblyName": "GCF_000307795.1",
          "color": "rgba(30,132,132,0.14)"
        },
        {
          "refName": "NC_018939v1",
          "start": 804000,
          "end": 824000,
          "assemblyName": "GCF_000307795.1",
          "color": "rgba(214,40,40,0.12)"
        }
      ],
      "tracks": [
        {
          "trackId": "hpylori_repl_origin",
          "height": 50,
          "encoding": {
            "color": {
              "value": "jexl:get(feature,'color')"
            }
          }
        },
        "gc_content_hpylori",
        "gc_skew_hpylori"
      ]
    }
  ]
}
JSON

cat > callouts.json <<'JSON'
[
  {
    "type": "text",
    "text": "leading strand",
    "anchor": {
      "trackId": "gc_skew_hpylori",
      "loc": "NC_018939v1:166,800",
      "fracY": 0.11
    },
    "maxWidth": 260
  },
  {
    "type": "text",
    "text": "lagging strand",
    "anchor": {
      "trackId": "gc_skew_hpylori",
      "loc": "NC_018939v1:1,034,100",
      "fracY": 0.89
    },
    "maxWidth": 260
  },
  {
    "type": "text",
    "text": "terminus",
    "leader": true,
    "anchor": {
      "trackId": "gc_skew_hpylori",
      "loc": "NC_018939v1:814,000",
      "fracY": 0.45
    },
    "dx": 60,
    "dy": -45,
    "maxWidth": 220
  },
  {
    "type": "text",
    "text": "origin",
    "leader": true,
    "anchor": {
      "trackId": "gc_skew_hpylori",
      "loc": "NC_018939v1:1,608,000",
      "fracY": 0.45
    },
    "dx": -60,
    "dy": -45,
    "maxWidth": 220
  }
]
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/hpylori/config.json \
  --width 1500 --height 800 \
  --spec session.json --annotations callouts.json -o figure.png

More: Using JBrowse with AI agents.

Adds these tracks to your config.json, styled as in the figure. Point each uri at your file.

jbrowse add-track-json '{
  "type": "GCContentTrack",
  "trackId": "gc_content_hpylori",
  "name": "GC content",
  "assemblyNames": [
    "GCF_000307795.1"
  ],
  "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"
      }
    },
    "op": "content",
    "window": 2000,
    "step": 2000
  }
}'

jbrowse add-track-json '{
  "type": "GCContentTrack",
  "trackId": "gc_skew_hpylori",
  "name": "GC skew",
  "assemblyNames": [
    "GCF_000307795.1"
  ],
  "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"
      }
    },
    "op": "skew",
    "window": 20000,
    "step": 2000
  },
  "displays": [
    {
      "type": "LinearWiggleDisplay",
      "displayId": "gc_skew_hpylori-LinearWiggleDisplay",
      "height": 160
    }
  ]
}'

jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "hpylori_repl_origin",
  "name": "Replication origin / terminus (from GC skew)",
  "assemblyNames": [
    "GCF_000307795.1"
  ],
  "adapter": {
    "type": "FromConfigAdapter",
    "features": [
      {
        "refName": "NC_018939v1",
        "uniqueId": "oriC",
        "start": 1598000,
        "end": 1618000,
        "name": "oriC (dnaA)",
        "color": "#1e8484"
      },
      {
        "refName": "NC_018939v1",
        "uniqueId": "terminus",
        "start": 804000,
        "end": 824000,
        "name": "terminus",
        "color": "#d62828"
      }
    ]
  },
  "displayDefaults": {
    "height": 50,
    "encoding": {
      "color": {
        "value": "jexl:get(feature,'\''color'\'')"
      }
    }
  }
}'

Run beside config.json, or add --out <dir>. Needs GCF_000307795.1 in the config (jbrowse add-assembly).

This view in a notebook, with jbrowse-anywidget. Swap a track's uri for your file.

from jbrowse_anywidget import JBrowseApp, fetch_hub

config = fetch_hub("https://jbrowse.org/demos/hpylori/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []) + [
        {
            "type": "GCContentTrack",
            "trackId": "gc_content_hpylori",
            "name": "GC content",
            "assemblyNames": [
                "GCF_000307795.1"
            ],
            "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"
                    }
                },
                "op": "content",
                "window": 2000,
                "step": 2000
            }
        },
        {
            "type": "GCContentTrack",
            "trackId": "gc_skew_hpylori",
            "name": "GC skew",
            "assemblyNames": [
                "GCF_000307795.1"
            ],
            "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"
                    }
                },
                "op": "skew",
                "window": 20000,
                "step": 2000
            },
            "displays": [
                {
                    "type": "LinearWiggleDisplay",
                    "displayId": "gc_skew_hpylori-LinearWiggleDisplay",
                    "height": 160
                }
            ]
        },
        {
            "type": "FeatureTrack",
            "trackId": "hpylori_repl_origin",
            "name": "Replication origin / terminus (from GC skew)",
            "assemblyNames": [
                "GCF_000307795.1"
            ],
            "adapter": {
                "type": "FromConfigAdapter",
                "features": [
                    {
                        "refName": "NC_018939v1",
                        "uniqueId": "oriC",
                        "start": 1598000,
                        "end": 1618000,
                        "name": "oriC (dnaA)",
                        "color": "#1e8484"
                    },
                    {
                        "refName": "NC_018939v1",
                        "uniqueId": "terminus",
                        "start": 804000,
                        "end": 824000,
                        "name": "terminus",
                        "color": "#d62828"
                    }
                ]
            }
        }
    ],
    views=[
        {
            "type": "LinearGenomeView",
            "assembly": "GCF_000307795.1",
            "loc": "NC_018939v1",
            "highlight": [
                {
                    "refName": "NC_018939v1",
                    "start": 1598000,
                    "end": 1618000,
                    "assemblyName": "GCF_000307795.1",
                    "color": "rgba(30,132,132,0.14)"
                },
                {
                    "refName": "NC_018939v1",
                    "start": 804000,
                    "end": 824000,
                    "assemblyName": "GCF_000307795.1",
                    "color": "rgba(214,40,40,0.12)"
                }
            ],
            "tracks": [
                {
                    "trackId": "hpylori_repl_origin",
                    "height": 50,
                    "encoding": {
                        "color": {
                            "value": "jexl:get(feature,'color')"
                        }
                    }
                },
                "gc_content_hpylori",
                "gc_skew_hpylori"
            ]
        }
    ],
)
app  # display the widget

jbrowse-img draws this view as an SVG, no browser needed. Swap --config or a track for your own.

cat > tracks.json <<'JSON'
[
  {
    "type": "GCContentTrack",
    "trackId": "gc_content_hpylori",
    "name": "GC content",
    "assemblyNames": [
      "GCF_000307795.1"
    ],
    "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"
        }
      },
      "op": "content",
      "window": 2000,
      "step": 2000
    }
  },
  {
    "type": "GCContentTrack",
    "trackId": "gc_skew_hpylori",
    "name": "GC skew",
    "assemblyNames": [
      "GCF_000307795.1"
    ],
    "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"
        }
      },
      "op": "skew",
      "window": 20000,
      "step": 2000
    },
    "displays": [
      {
        "type": "LinearWiggleDisplay",
        "displayId": "gc_skew_hpylori-LinearWiggleDisplay",
        "height": 160
      }
    ]
  },
  {
    "type": "FeatureTrack",
    "trackId": "hpylori_repl_origin",
    "name": "Replication origin / terminus (from GC skew)",
    "assemblyNames": [
      "GCF_000307795.1"
    ],
    "adapter": {
      "type": "FromConfigAdapter",
      "features": [
        {
          "refName": "NC_018939v1",
          "uniqueId": "oriC",
          "start": 1598000,
          "end": 1618000,
          "name": "oriC (dnaA)",
          "color": "#1e8484"
        },
        {
          "refName": "NC_018939v1",
          "uniqueId": "terminus",
          "start": 804000,
          "end": 824000,
          "name": "terminus",
          "color": "#d62828"
        }
      ]
    }
  }
]
JSON

npx @jbrowse/img --config https://jbrowse.org/demos/hpylori/config.json \
  --tracks tracks.json \
  --assembly GCF_000307795.1 --loc NC_018939v1 \
  --view '{"highlight":[{"refName":"NC_018939v1","start":1598000,"end":1618000,"assemblyName":"GCF_000307795.1","color":"rgba(30,132,132,0.14)"},{"refName":"NC_018939v1","start":804000,"end":824000,"assemblyName":"GCF_000307795.1","color":"rgba(214,40,40,0.12)"}]}' \
  --track hpylori_repl_origin '{"height":50,"encoding":{"color":{"value":"jexl:get(feature,'\''color'\'')"}}}' \
  --track gc_content_hpylori \
  --track gc_skew_hpylori \
  --width 1500 --out figure.svg

For a PNG, --out figure.png (needs rsvg-convert: apt install librsvg2-bin, brew install librsvg).

The session spec behind the figure, over this config.

{
  "sessionTracks": [
    {
      "type": "GCContentTrack",
      "trackId": "gc_content_hpylori",
      "name": "GC content",
      "assemblyNames": [
        "GCF_000307795.1"
      ],
      "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"
          }
        },
        "op": "content",
        "window": 2000,
        "step": 2000
      }
    },
    {
      "type": "GCContentTrack",
      "trackId": "gc_skew_hpylori",
      "name": "GC skew",
      "assemblyNames": [
        "GCF_000307795.1"
      ],
      "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"
          }
        },
        "op": "skew",
        "window": 20000,
        "step": 2000
      },
      "displays": [
        {
          "type": "LinearWiggleDisplay",
          "displayId": "gc_skew_hpylori-LinearWiggleDisplay",
          "height": 160
        }
      ]
    },
    {
      "type": "FeatureTrack",
      "trackId": "hpylori_repl_origin",
      "name": "Replication origin / terminus (from GC skew)",
      "assemblyNames": [
        "GCF_000307795.1"
      ],
      "adapter": {
        "type": "FromConfigAdapter",
        "features": [
          {
            "refName": "NC_018939v1",
            "uniqueId": "oriC",
            "start": 1598000,
            "end": 1618000,
            "name": "oriC (dnaA)",
            "color": "#1e8484"
          },
          {
            "refName": "NC_018939v1",
            "uniqueId": "terminus",
            "start": 804000,
            "end": 824000,
            "name": "terminus",
            "color": "#d62828"
          }
        ]
      }
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "GCF_000307795.1",
      "loc": "NC_018939v1",
      "highlight": [
        {
          "refName": "NC_018939v1",
          "start": 1598000,
          "end": 1618000,
          "assemblyName": "GCF_000307795.1",
          "color": "rgba(30,132,132,0.14)"
        },
        {
          "refName": "NC_018939v1",
          "start": 804000,
          "end": 824000,
          "assemblyName": "GCF_000307795.1",
          "color": "rgba(214,40,40,0.12)"
        }
      ],
      "tracks": [
        {
          "trackId": "hpylori_repl_origin",
          "height": 50,
          "encoding": {
            "color": {
              "value": "jexl:get(feature,'color')"
            }
          }
        },
        "gc_content_hpylori",
        "gc_skew_hpylori"
      ]
    }
  ]
}

GC content vs GC skew

GC parameters → GC content and GC parameters → GC skew switch between the two calculations (the adapter's op slot):

  • GC content is the fraction of A, C, G and T bases in each window that are G or C, 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 sets the sliding window:

  • 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 follows zoom, on by default, places about one point per pixel, so zoomed out each point covers more bases. Where the step is wider than the window, the window widens to the step, and every base counts toward a point.
  • Turning it off shows a Step size slider for a fixed distance between successive windows. A step smaller than the window overlaps the windows, which gives a smoother curve at the cost of more points to compute. The slider's reset turns Step follows zoom back on.

N and the other ambiguity codes count toward neither the GC bases nor the total, so the track draws nothing over an assembly gap.

Zoomed out across a whole chromosome, the track still reads every base of it. For a large genome viewed whole, a precomputed GC bigWig such as UCSC's gc5Base loads faster.

Display options

The GC content track is a quantitative (wiggle) track, so it inherits the full set of quantitative track display options from the same track menu: bar plot / line / density / scatter rendering, linear vs log scale, outlier clipping, and manual min/max.

See also