# LGVSyntenyDisplay Auto-generated config schema for the current JBrowse release — see the [config guide](https://jbrowse.org/jb2-staging/docs/config_guide) for concepts. Provided by the `linear-comparative-view` plugin. [View source](https://github.com/GMOD/jbrowse-components/blob/main/plugins/linear-comparative-view/src/LGVSyntenyDisplay/configSchemaF.ts). ## 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: ```js { 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._ ## Related links - **Adapter:** [AllVsAllIndexedPAFAdapter](../allvsallindexedpafadapter) - **Adapter:** [AllVsAllPAFAdapter](../allvsallpafadapter) - **Adapter:** [BlastTabularAdapter](../blasttabularadapter) - **Adapter:** [ChainAdapter](../chainadapter) - **Adapter:** [DeltaAdapter](../deltaadapter) - **Adapter:** [MashMapAdapter](../mashmapadapter) - **Adapter:** [MCScanAnchorsAdapter](../mcscananchorsadapter) - **Adapter:** [MCScanBlocksAdapter](../mcscanblocksadapter) - **Adapter:** [MCScanSimpleAnchorsAdapter](../mcscansimpleanchorsadapter) - **Adapter:** [PAFAdapter](../pafadapter) - **Adapter:** [PairwiseIndexedPAFAdapter](../pairwiseindexedpafadapter) - **State model:** [runtime API](../../models/lgvsyntenydisplay) - **Base config:** [LinearAlignmentsDisplay](../linearalignmentsdisplay) ## Config slots These slots go on a display entry: `"displays": [{ "type": "LGVSyntenyDisplay", ... }]`, or in the track's [`displayDefaults`](https://jbrowse.org/jb2-staging/docs/config_guides/tracks#configuring-displays) when this is its default display. Slot types (`fileLocation`, `frozen`, ...) are explained in the [config slot types reference](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types). Slots a base configuration contributes are listed here too, so this table is the whole surface. | Slot | Description | | --- | --- | | **mouseover**
[`string`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#string) = 'jexl:lgvSyntenyTooltip(feature)' | Tooltip shown on hovering a synteny feature; the default jexl expression renders both mates' names and locations.
_callback args:_ `feature` | | **colorBy**
[`maybeFrozen`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#the-maybe-types) = { type: 'strand' } _promotable_ | Synteny reads are strand-colored by default (vs the base alignments display's `normal`); overrides the inherited `colorBy` slot's default.
_advanced_ | | **showCoverage**
[`boolean`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#boolean) = false | Synteny reads hide the coverage histogram by default; overrides the inherited base alignments display's `showCoverage` default of `true`. | | **collapseGroupRows**
[`boolean`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#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`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#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. | | **largeFeaturesFirst**
[`boolean`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#boolean) = true | 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 `largeFeaturesFirst` default of `false`. | | Inherited from [LinearAlignmentsDisplay](../linearalignmentsdisplay) | 44 slots | | **featureHeight**
[`maybeNumber`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#the-maybe-types) = 7 _promotable_ | Height of each feature (read) in pixels. Unset (the default) follows the session-wide default for this display type, falling back to 7; an explicit number customizes the track (including customizing 7 back over a compact session default) | | **readConnectionsLineWidth**
[`number`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#number) = 1 | Line width for read-connection arcs/lines in pixels | | **showSashimiLabels**
[`maybeBoolean`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#the-maybe-types) = false _promotable_ | Draw the supporting-read count on each sashimi arc | | **hideNonCanonicalJunctions**
[`maybeBoolean`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#the-maybe-types) = false _promotable_ | 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`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#number) = 6000 | Maximum pixel height of the pileup layout; reads beyond this are not stacked (coverage still reflects true depth)
_advanced_ | | **height**
[`number`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#number) = 250 | Starting height in pixels for the coverage band and pileup together; heightMode decides what a pileup deeper than this does | | **filterBy**
[`frozen`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#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_ | | **groupBy**
[`frozen`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#frozen) = null | In-track stacked grouping, e.g. `{ type: "strand" }` to pre-group reads by strand (null = ungrouped)
_advanced_ | | **autoscale**
[`stringEnum`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#stringenum) (local, localsd) = 'local' | Coverage autoscale type | | **minScore**
[`number`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#number) = Number.MIN_VALUE | Minimum coverage depth bound
_advanced_ | | **maxScore**
[`number`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#number) = Number.MAX_VALUE | Maximum coverage depth bound
_advanced_ | | **scaleType**
[`stringEnum`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#stringenum) (linear, log, symlog) = 'linear' | Coverage scale type. "log" floors the domain at a depth of 1, which draws a single-read position at the same height as no coverage at all; "symlog" is log-like higher up and linear through zero, so low depths stay separable | | **symlogConstant**
[`number`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#number) = 1 | Width of symlog's linear region around zero, in depth units. The default 1 makes symlog exactly log(depth+1), which is the transform read depth wants: the knee sits at one read, the smallest depth there is. 0 means "derive from the domain" (a thousandth of the visible max) — right for a wiggle track, whose units are its own, and wrong here, since it puts the knee a tenth of a read below zero and draws a single stray read a third of the way up a depth-100 band
_advanced_ | | **numStdDev**
[`number`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#number) = 3 | Number of standard deviations for localsd autoscale
_advanced_ | | **mismatchAlpha**
[`maybeBoolean`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#the-maybe-types) = false _promotable_ | Fade mismatch bases by their per-base Phred quality. Unset (the default) follows the session-wide default for this display type, falling back to off; an explicit true/false customizes the track (either direction, including customizing off over an on session default) | | **showLowFreqMismatches**
[`boolean`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#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**
[`maybeBoolean`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#the-maybe-types) = false _promotable_ | Show the color-scheme legend overlay. Unset (the default) follows the session-wide default for this display type, falling back to off; an explicit true/false customizes the track (either direction, including customizing off over an on session default) | | **sortedBy**
[`frozen`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#frozen) = null | Sort reads at a genomic position, e.g. by base, strand, or a tag (null = unsorted)
_advanced_ | | **splicedReadsFirst**
[`boolean`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#boolean) = false | The other layout-order flag, for RNA-seq: reads whose CIGAR carries a skip take the lowest rows. Ignored while a `sortedBy` position sort is active; wins over `largeFeaturesFirst` if both are set. | | **showOutline**
[`frozen`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#frozen) = null | 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**
[`maybeStringEnum`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#the-maybe-types) (off, normal) = 'off' _promotable_ | View as pairs / link supplementary alignments: put a read, its mate and its split segments on one row | | **showBezierConnections**
[`boolean`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#boolean) = false | Draw paired-read connection curves over the pileup | | **showPileup**
[`boolean`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#boolean) = true | Draw the stacked-read pileup band | | **coverageHeight**
[`number`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#number) = 45 | Height of the coverage band in pixels | | **coverageSnpMinFrequency**
[`number`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#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`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#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_LAYERS) | | **showInterbaseIndicators**
[`boolean`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#boolean) = true | Draw interbase insertion/clip count bars and indicator triangles | | **flipStrandLongReadChains**
[`boolean`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#boolean) = true | Color split segments relative to the predominant orientation of the reads on screen, rather than by their own mapping strand | | **colorSupplementaryChains**
[`boolean`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#boolean) = false | Paint every chain carrying a supplementary segment a flat supplementary color, paired or not | | **drawInter**
[`boolean`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#boolean) = true | Draw inter-chromosomal read-connection arcs | | **drawProperPairArcs**
[`boolean`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#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`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#number) = 2 | Hide inter-chromosomal connections supported by fewer than this many reads clustered at the same breakpoint | | **drawLongRange**
[`boolean`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#boolean) = true | Draw long-range read-connection arcs | | **arcColorByType**
[`stringEnum`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#stringenum) (insertSizeAndOrientation, insertSize, orientation) = 'insertSizeAndOrientation' | How to color read-connection arcs | | **readConnections**
[`maybeStringEnum`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#the-maybe-types) (off, arc, cloud) = 'off' _promotable_ | Read-connection rendering mode (mate pairs + split reads) | | **readConnectionsDown**
[`maybeBoolean`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#the-maybe-types) = true _promotable_ | Draw read connections below the coverage band. Unset (the default) follows the session-wide default for this display type, falling back to on; an explicit true/false customizes the track (either direction, including drawing above the coverage band over an on session default) | | **showSashimiArcs**
[`maybeBoolean`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#the-maybe-types) = true _promotable_ | Draw sashimi (splice-junction) arcs | | **sashimiArcsMode**
[`maybeStringEnum`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#the-maybe-types) (up, down, auto) = 'up' _promotable_ | Sashimi junction-arc placement | | **minSashimiScore**
[`number`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#number) = 2 | Hide sashimi arcs with fewer than this many supporting reads | | **sashimiArcsHeight**
[`number`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#number) = 40 | Height of the sashimi-arc band in pixels | | **readConnectionsHeight**
[`number`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#number) = 35 | Height of the read-connection band in pixels | | **showSoftClipping**
[`maybeBoolean`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#the-maybe-types) = false _promotable_ | Draw soft-clipped read portions. Unset (the default) follows the session-wide default for this display type, falling back to off; an explicit true/false customizes the track (either direction, including customizing off over an on session default) | | **heightMode**
[`maybeStringEnum`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#the-maybe-types) (fixed, grow, fit) = 'fixed' _promotable_ | 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). Unset (the default) follows the session-wide default for this display type, falling back to `fixed`; `fixed` 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`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#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_ | | Inherited from [BaseLinearDisplay](../baselineardisplay) | 4 slots | | **maxFeatureScreenDensity**
[`number`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#number) = 1 | maximum features per pixel before showing a "too many features" message
_advanced_ | | **jexlFilters**
`stringArray` = [] | config jexlFilters are deferred evaluated so they are prepended with jexl at runtime rather than being stored with jexl in the config | | **fetchSizeLimit**
[`number`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#number) = 1_000_000 | maximum data to attempt to download for a given track, used if adapter doesn't specify one
_advanced_ | | **forceLoad**
[`boolean`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#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_ |