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Annotation and coordinates

Plots that name what lies along a sequence and show how to read positions on it: gene models, transcription units, reading frames, rulers in bases or codons, and a key to the colours.

How to choose

Your question Plot Build it with
Where are the genes, exons, repeats or primers? Features FeatureTrack, --features
Which genes share one transcript, and where does it start and stop? Transcription units TranscriptionUnitTrack, Rust only
Could an unannotated stretch be coding, and on which strand? Six reading frames OrfTrack, --orfs
Which position is this, as a genome browser would number it? Coordinate ruler AxisTrack, added at the bottom by plot() and by the command line; --axis places it
Which residue is this, as in S450L or V600E? Codon ruler CodonTrack, --codons
What do the colours and shapes stand for? Legend LegendTrack, Rust only

Plots

  • A depth profile, a reference band, the rpoB gene with its resistance-determining region as a second, stranded feature on a row of its own, and variant calls

    Features Intervals from BED or GFF3 packed into as few rows as the zoom allows, with strand shown by an arrowhead and by the strand colours the other tracks use.

  • Three transcription units over the ESX-1 genes of M. tuberculosis, each a bent arrow at its start site with a hairpin or a bar at its end, one of them leaderless, above the gene models

    Transcription units One RNA from its start site through its leader to its terminator, so the genes in a feature track beneath it read as transcribed together.

  • Six reading frames across three and a half kilobases, stop codons as ticks and open stretches as bars, forward frames above the line and reverse frames below

    Six reading frames Stops and open stretches in all six frames, worked out from the sequence alone; requiring a start codon is a separate switch, off by default.

  • Two figures over the rpoB locus, each ending in a coordinate ruler labelled in kilobases: depth, annotation and allele frequencies above, a centred strand-composition score below

    Coordinate ruler Round, 1-based tick labels in one unit for the whole ruler: the numbers you would type into a genome browser.

  • rpoB codons 439 to 465 numbered and translated, with variant lollipops over codons 445 and 450 and a base ruler underneath

    Codon ruler Codons numbered and translated along a coding sequence, counting from the far end on the reverse strand, so a change can be named by its residue.

  • One gene cluster in three genomes joined by identity ribbons, with a legend band beneath it: a filled swatch for the deleted block, an identity ramp and an outline for genes with no match

    Legend A key as a band of its own, placed where you push it and wrapped onto another row rather than dropping an entry.