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LGVSyntenyDisplay

Auto-generated config schema for the current JBrowse release — see the config guide for concepts. Provided by the linear-comparative-view plugin. View source.

Example usage

Shows a SyntenyTrack's alignments in a plain linear view (rather than the two-row synteny view). Same track config as a synteny track — just pick this display type:

{
  type: 'SyntenyTrack',
  trackId: 'hg38_vs_mm10',
  name: 'hg38 vs mm10',
  assemblyNames: ['hg38', 'mm10'],
  adapter: {
    type: 'PAFAdapter',
    uri: 'https://example.com/hg38_vs_mm10.paf',
    queryAssembly: 'hg38',
    targetAssembly: 'mm10',
  },
  displays: [
    {
      type: 'LGVSyntenyDisplay',
      displayId: 'hg38_vs_mm10-LGVSyntenyDisplay',
    },
  ],
}

See the Config slots section below for all available configuration fields.

Config slots

These slots go on a display entry: "displays": [{ "type": "LGVSyntenyDisplay", ... }], or in the track's displayDefaults when this is its default display. Slot types (fileLocation, frozen, ...) are explained in the config slot types reference. Slots a base configuration contributes are listed here too, so this table is the whole surface.

SlotDescription
lodMode
stringEnum (auto, fine, coarse) = 'auto'		which stored tier of a tiered file is fetched: 'auto' switches on the adapter's bpPerPx threshold, 'fine' pins the per-row CIGAR tier, and 'coarse' the tier whose CIGAR is folded to its large indels
mouseover
string = 'jexl:lgvSyntenyTooltip(feature)'		Tooltip shown on hovering a synteny feature; the default jexl expression renders both mates' names and locations.
callback args: feature
color
LGVSyntenyColor		The alignments displays' color object with field defaulting to strand, where the base display paints the plain fill.
showCoverage
boolean = false		Synteny reads hide the coverage histogram by default; overrides the inherited base alignments display's showCoverage default of true.
collapseGroupRows
boolean = true		One lane per group by default: an all-vs-all track grouped by mate assembly draws each mate genome as a single band, with repeat depth shown as darker shading rather than as extra rows. Overrides the base alignments display's collapseGroupRows default of false, where a group is a read category and the stack itself is the information.
hideSelfAlignments
boolean = false		Hide the lane an all-vs-all track draws for the view's own assembly. That lane holds no self-alignment line — aligners skip each sequence's own diagonal — so it carries only the assembly's internal paralogy, and readers consistently read it as missing data. Only meaningful when grouping by mate assembly.
layoutOrder
stringEnum (position, length, spliced) = 'length'		Synteny lays large alignments out first so big syntenic blocks cluster at the top instead of interleaving with small ones; overrides the base alignments display's position default.
Inherited from LinearAlignmentsDisplay42 slots
featureHeight
number = 7		Height of each feature (read) in pixels. Defaults to 7
readConnectionsLineWidth
number = 1		Line width for read-connection arcs/lines in pixels
showSashimiLabels
boolean = false		Draw the supporting-read count on each sashimi arc
hideNonCanonicalJunctions
boolean = false		Hide sashimi arcs whose splice-site motif is none of GT-AG, GC-AG or AT-AC. Read off the reference under each junction, so it needs a sequence adapter; a junction whose motif could not be read stays
maxHeight
number = 6000		Maximum pixel height of the pileup layout; reads beyond this are not stacked (coverage still reflects true depth)
advanced
height
number = 250		Starting height in pixels for the coverage band and pileup together; heightMode decides what a pileup deeper than this does
baseColor
AlignmentsBaseColor		The per-base layer drawn over the reads, whatever fills them: { field: "modifications" }, "bisulfite", "baseQuality" or "base".
modifications
frozen = {}		What the modifications and bisulfite colour fields draw: threshold (percent, default 10), twoColor, fillUnmarked, cytosineContext and shownModifications; see the ModificationColorBy type.
advanced
filterBy
frozen = defaultFilterFlags		Every read filter, in one object: the flag masks, a read name, tag filters, and the four read categories.

default filter flags is exclude 1540 read unmapped (0x4) read fails platform/vendor quality checks (0x200) read is PCR or optical duplicate (0x400)

A read category takes "only" or "exclude", and is absent when it isn't filtering — { "properPairs": "exclude", "split": "only" } for the split reads of discordant pairs. spliced, properPairs, singletons and split; see the FilterBy type.
advanced
facet
Facet		In-track stacked grouping, one labelled section per value: a read dimension (strand, firstOfPairStrand, pairOrientation, splitRead, mapq, mateAssembly), a tag (tags.HP), or any other field. { field: "tags.HP", domain: ["2", "1"] } stacks the listed values first.
scales
ValueScale		The coverage band's value scale — the one thing on this display drawn against an axis, the pileup having no value and the arcs their own arcBandYScale. symlogConstant starts at 1 rather than the wiggle family's 0, which makes symlog exactly log(depth+1): the knee sits at one read, the smallest depth there is. domainQuantile stays at 1, the deepest base in view: 0.99, which Clip outliers writes, cuts the tallest stretch of even flat coverage in every view, and misses a collapsed-repeat pile-up once it covers more than 1% of the view.
mismatchAlpha
boolean = false		Fade mismatch bases by their per-base Phred quality. Defaults to off
showLowFreqMismatches
boolean = false		Draw sub-pixel mismatches, insertions and clip bars in the pileup at full opacity instead of fading the ones below the depth-dependent frequency threshold. Read through the filterMismatchesByFrequency getter, which is this in the polarity the renderers and hit-test take. Does not affect the coverage band (see runCoveragePipeline)
advanced
showLegend
boolean = false		Show the color-scheme legend overlay. Defaults to off
sortedBy
maybeFrozen		Sort reads at a genomic position, e.g. by base, strand, or a tag (unset = unsorted)
advanced
showOutline
maybeFrozen		null = auto: outline is drawn only in chain/linked-read modes. Set true/false to force it on or off regardless of mode.
advanced
linkedReads
stringEnum (off, normal) = 'off'		View as pairs / link supplementary alignments: put a read, its mate and its split segments on one row
showBezierConnections
boolean = false		Draw paired-read connection curves over the pileup
showPileup
boolean = true		Draw the stacked-read pileup band
coverageHeight
number = 45		Height of the coverage band in pixels
coverageSnpMinFrequency
number = 0		Hide a coverage-band allele segment whose share of that position's depth is below this fraction, so the band stops painting a sliver for every sequencing error at high depth. 0 (the default) colors every mismatch. Distinct from showLowFreqMismatches, which turns OFF the pileup's fade of sub-pixel marks against a depth-dependent threshold; this is a flat allele-fraction floor on the band, and the grey depth bar still shows through where a segment is hidden
advanced
showMismatches
boolean = true		Draw how reads differ from the reference: per-base mismatches, insertion markers and deletion bars. Not the intron centerlines — a spliced read is drawn as separate exon blocks, so the line joining them says they are one read rather than several, and it draws either way (PILEUP_MARKS)
showInterbaseIndicators
boolean = true		Draw interbase insertion/clip count bars and indicator triangles
flipStrandLongReadChains
boolean = true		Color split segments relative to the predominant orientation of the reads on screen, rather than by their own mapping strand
colorSupplementaryChains
boolean = false		Paint every chain carrying a supplementary segment a flat supplementary color, paired or not
drawInter
boolean = true		Draw inter-chromosomal read-connection arcs
drawProperPairArcs
boolean = true		Draw arcs for ordinary concordant pairs. Uncheck to leave only the arcs that carry a category (abnormal insert size or orientation, split junctions), which on deep coverage is the difference between a readable band and a solid mass
minInterchromSupport
number = 2		Hide inter-chromosomal connections supported by fewer than this many reads clustered at the same breakpoint
drawLongRange
boolean = true		Draw long-range read-connection arcs
arcColor
AlignmentsArcColor		What colours the read-connection arcs and the read cloud: "pairOrientation" paints them by pair orientation whatever the reads show, and "" takes the reads' color field where an arc paints it.
readConnections
stringEnum (off, arc, cloud) = 'off'		Read-connection rendering mode (mate pairs + split reads)
readConnectionsDown
boolean = true		Draw read connections below the coverage band. Defaults to on
showSashimiArcs
boolean = true		Draw sashimi (splice-junction) arcs
sashimiArcsMode
stringEnum (up, down, auto) = 'up'		Sashimi junction-arc placement
minSashimiScore
number = 2		Hide sashimi arcs with fewer than this many supporting reads
sashimiArcsHeight
number = 40		Height of the sashimi-arc band in pixels
readConnectionsHeight
number = 35		Height of the read-connection band in pixels
showSoftClipping
boolean = false		Draw soft-clipped read portions. Defaults to off
heightMode
stringEnum (fixed, grow, fit) = 'fixed'		Track-sizing strategy — how the track responds when there are more reads than fit (shared vocabulary with the canvas feature display, exposed in the "Track sizing" menu). fixed (the default) keeps featureHeight and scrolls; grow expands the track to show every read at the configured height; fit squeezes reads so every uncollapsed group fills the display without scrolling. Orthogonal to the per-read size set by featureHeight
growMaxHeight
number = 800		Ceiling in pixels for the "autogrow track height" sizing mode; a pileup deeper than this grows to the ceiling and scrolls the rest. Does not apply to the fixed or fit modes, and does not limit how much is laid out (see maxHeight)
advanced
densityTier
stringEnum (auto, features, density) = 'auto'		when to draw the features-per-bin density band in place of features: "auto" swaps to it where the region is too large to fetch, "features" never does and keeps the banner, "density" always does. Needs a density source on the adapter (its densityAdapter slot)
advanced
densityTierBpPerPx
number = 0		in "auto" mode, also draw the density band from this many bp per pixel outward, before the region is too large to fetch; 0 leaves the swap to the fetch-size gate alone
advanced
Inherited from BaseLinearDisplay2 slots
fetchSizeLimit
number = 1_000_000		maximum data to attempt to download for a given track, used if adapter doesn't specify one
advanced
forceLoad
boolean = false		Declarative equivalent of the "Force load" button on the "too much data" banner: when true the display always renders, however large the region or dense the features. Off by default (the gate guards against huge downloads). Set it on a view no one can interact with — an embedded / notebook view, or a screenshot — where the region is known and you want it drawn without a click.
advanced