Graphical View Legend

This legend is used by both NCBI Sequence Viewer and NCBI Genome Workbench.

  1. Genetic Feature Rendering
  2. Gene Model Features
  3. Clone Placement Features
  4. SNP Features
  5. Structural Variants
  6. Segmental Duplications
  7. Alignments
  8. Sequence Track
  9. Segment Map
  10. Six Frame Translations
  11. Label Placement
  12. Histogram or Graph Rendering
  13. Trace Graph Rendering

1. Generic Feature Rendering

This section describes the rendering used for gene features, RNA and protein models, regulatory sites, and most other feature types. These features often derive from files formatted as BED, bigBED, GFF3, GTF, ASN.1, and similar formats.

Specialized rendering for SNPs, structural variants, and segmental duplications are described in the later sections of this documentation.

1.1 Feature Color Code

Feature Type Color Visual Examples
Miscellaneous features purple purple Example
Regulatory teal teal Example
Protein binding site red red Example
Recombination golden brown golden brown Example
Mobile genetic element blue blue Example
Repeat region blue blue Example
Mature peptide golden brown golden brown Example
Gene Green Green Example
RNA Purple Purple Example
Coding Region Red Red Example
All other features Black Black Example

White arrows inside features indicate the direction of the feature relative to the top-level sequence. Grey arrows in introns (e.g. in RNA and coding region features) indicate the direction of splicing.

1.2 Special Rendering Styles

1.2.1 Pseudogene features

Display Settings Visual Effect Visual Examples
Show all Stripes within green gene bar Stripes over green gene bar
No gene bar Green stripe background Green stripe background
Show on single line with exon structure, no gene bar Green stripe background Green stripe background

1.2.2 Features with imperfect match to the assembly

Example Visual Effect Visual Examples
RNA or CDS feature with sequence discrepancy relative to the assembly Shaded background Mismatch in transcription

1.2.3 Features with partial annotation location (e.g. due to assembly errors or gaps)

Examples Visual Effect Visual Examples
Partial 5’ end Black arrows ("<<" or ">>") at 5' end Partial Start
Partial 3’ end Black arrows ("<<" or ">>") at 3' end Partial End
Internal imprecise ends Black arrows (“<<” and “>>”) at internal junctions Partial Start and Stop
Partial 5’ and 3’ ends Black arrows ("<<" and ">>") at both ends Partial Start and Stop

1.2.4 Feature marked as partial

Example Cases Visual Effect Visual Examples
Feature marked as partial at 5’ and 3’ ends (white arrows, "<<" and ">>") and feature with a partial 3' end (black arrows ">>") White arrows ("<<" and ">>") at both ends or black arrows (">>") at one end. 1.2.4_1

1.2.5 Restriction site features

Restriction enzyme recognition sites are rendered with triangle marks indicating the cut sites. Triangle marks are not present at high zoom levels. When the feature is selected using a mouse click, the location of the cut sites is indicated by red hairlines.

View Visual Effect Visual Examples
Restriction enzyme recognition site Triangles indicate cut sites 1.2.5_1
Restriction site (feature selected) Triangles indicate cut site; hairlines mark feature boundaries and cut sites 1.2.5_2
Restriction site (feature selected, zoomed out) No triangles; hairlines mark feature boundaries and cut sites 1.2.5_3

1.3 Feature Decorations

Decor Style Visual Effect Visual Examples
Default Solid bars for feature intervals or exons, and solid lines for introns Solid bars for feature intervals or exons, and solid lines for introns
Arrows Arrows at both ends showing the strand, and shaded bars for introns Arrows at both ends showing the strand, and lighten bars for introns
Square Anchor Square for feature start, arrow for feature stop, dashed lines for introns Square for feature start, arrow for feature stop, dash lines for introns
Circle Anchor Circle for feature start, arrow for feature stop, dashed lines for introns Circle for feature start, arrow for feature stop, dash lines for introns
Fancy Circle for mRNA start only, square for other features start except for gene and CDS, arrow for feature stop, shaded bars for mRNA introns, and curvy lines for CDS introns Circle for mRNA start only, square for other features start except for gene and CDS, arrow for feature stop, lighten bars for mRNA introns, and canted lines for CDS introns

2. Gene Model Features

Gene model features are comprised of multiple possible components: gene bar, RNA/mRNA, CDS, and exon features. Gene models may also include SNPs and other features, such as protein domains, that can be projected from the aforementioned components. The track display settings dialog for gene feature tracks can be accessed by clicking on the track title or by selecting the track within the “Tracks” configuration menu.

tracks configuration menu

2.1 Gene Model Rendering

Track display settings include multiple rendering options as described below.

When all features are expanded, gene bars are colored green, non-coding RNAs and mRNA features are colored purple, and CDS features are colored red.

When transcript and CDS pairs are merged, the coding exons are rendered in dark green, and non-coding regions (i.e. 5’ and 3’ UTRs) are rendered in a lighter shade of green, and non-coding RNAs remain purple (See “Merge transcript and CDS pairs, no gene bar” example below).

When all transcripts are merged and merged features include exon portions that are present in some transcripts but missing in other transcripts, the intensity of the green coloring is proportional to the number of transcript variants that include a particular exon region (See “Merge all transcripts and CDSs, no gene bar” example below).

To show features annotated on the RNA or CDS, select the options to “Project SNPs from mRNA and CDS feature” and/or “Product Features”.

Rendering Options Visual Examples
Show All Show All
Show all transcripts and CDSs, no gene bar Show all transcripts and CDSs, no gene bar
Merge transcript and CDS pairs, no gene bar Merge transcript and CDS pairs, no gene bar
Merge all transcripts and CDSs, no gene bar Merge all transcripts and CDSs, no gene bar
Show on single line with exon structure Show on single line with exon structure
Gene bar only Gene bar only
Show all, with SNPs projected from mRNA and CDS features (in blue) With SNP features projected from mRNA and CDS products
Show all, with Product features projected from CDS features With other features projected from mRNA and CDS products

2.2 Special Rendering for discrepancies between RefSeq annotated sequences and genomic sequences

Rendering for mismatches

Screenshot of special rendering for CDS features

In the case of non-synonymous mismatches, the discrepancy is highlighted by a combination of red colored text for the codon, the display of the alternate bases in the mRNA feature, and the display of the alternate amino acid residue in the protein feature.

In the case of synonymous mismatches, the discrepancy is highlighted by a combination of red colored text for the codon, and the display of the alternate bases in the mRNA feature.

Rendering for insertions and deletions

rendering for discrepancies between annotated refseq and genomic sequences

Deletions appear as dash marks in the corresponding mRNA and protein features and lack any display of codons or amino acids.

Insertions appear as a pair of inverted vertical triangles in the mRNA and protein features, and the corresponding codons and amino acids are shown; codons are colored in red.

2.3 Feature Ruler

When all features are expanded in a gene model track, selecting an RNA or CDS feature by clicking on it will reveal a feature ruler indicating the local coordinates of the feature.

Screenshot of feature ruller

When multiple features are selected, hairlines appear that indicate differences in structure among the different features.

2.4 Feature Tooltip

Hovering over a feature reveals a tooltip with additional information about that feature. The tooltip for gene, RNA, and CDS features reports the feature length, span on the assembly, and the coordinate positions where the tooltip was activated. Links to other NCBI or external resources relating to the gene or feature are also included, where available. There are also options to download the feature in FASTA or GenBank formats, send it to BLAST, or open it in its own instance of the graphical sequence viewer. More information on gene tooltips is available here.

Feature Type Tooltip Example
RefSeq mRNA RefSeq mRNA
RefSeq CDS RefSeq CDS
RefSeq merged transcript and CDS RefSeq merged transcript and CDS
RefSeq gene bar RefSeq gene bar
Projected feature on CDS Projected feature on CDS

3. Clone Placement Features

3.1 Communicated Attributes

Graphical renderings for all clone placement features convey following attributes:

  • Concordancy
  • Uniqueness
  • Clone end confidence
  • Directionality, and
  • Supporting evidence

3.2 Visual examples for the conveyed attribute

Attribute Possible Values Rendering Visual Example
Clone placement type End-seq only 2 arrows joined by line Clone placement, end-seq only
Insert only Single arrow Clone placement, insert only
Combined end-seq and insert 2 arrows joined by line or single arrow on yellow background Clone placement, combined
Clone placement, combined
Concordancy Concordant Color: Blue Clone with no end, plus strand
Discordant Color: Red Clone with no end, plus strand
Concordancy not set Color: Gray Clone with no end, plus strand
End-seq only clone placement uniqueness Unique Connecting Line: solid Unique, discordant, Real ends
Multiple Connecting Line: dotted Multiple, discordant, Real ends
Uniqueness not set Connecting line: dashed Multiple, discordant, Real ends
Clone end confidence Unique Fill: solid color Clone with no end, plus strand
Multiple Fill: vertical bars Multiple, Concordant not set, Real ends
Virtual Fill: empty Multiple, Concordant not set, Real ends
Other/Not set Fill: horizontal bars Multiple, Concordant not set, Real ends
Insert only clone placement uniqueness Unique Fill: solid color Insert only, unique
Multiple Fill: vertical bars Insert only, multiple
Other/not set Fill: horizontal bars Insert only, other
Directionality Forward or Backward Arrow

Clone with no end, plus strand

Clone with no end, plus strand

Supporting Evidence All non-prototype ends are ‘supporting’ With no shaded background Unique, concordant, Real ends
Single, no shade
Two arrows, yellow shade
Single arrow, yellow shade
Not all non-prototype ends are ‘supporting’ With shaded background Unique, Discordant, One virtual end
Single arrow, gray background
Two arrows, yellow gray background
Sinhle, gray yellow shade

3.3 Rendering examples for various attribute combinations

The rendering is able to handle any combination of the five attributes shown above. Below are some rendering examples with various attribute combination.

Display Description
Unique, concordant, Real ends Unique, concordant, unique ends
Unique, concordant, Real ends Multiple, concordant, one unique end, one multiple end
Unique, concordant, Real ends Uniqueness-not-set, concordant, one multiple end, one confidence-not-set end
Unique, concordant, Real ends Unique, concordant, one confidence-not-set end, one virtual end
Unique, discordant, Real ends Unique, discordant, unique ends
Unique, concordant, Real ends Multiple, discordant, one unique end, one multiple end
Unique, concordant, Real ends Uniqueness-not-set, discordant, one multiple end, one confidence-not-set end
Unique, concordant, Real ends Unique, discordant, one confidence-not-set end, one virtual end
Unique, Concordant not set, Real ends Unique, concordancy not set, unique ends
Unique, concordant, Real ends Multiple, concordancy not set, one unique end, one multiple end
Unique, concordant, Real ends Uniqueness-not-set, concordancy not set, one multiple end, one confidence-not-set end
Unique, concordant, Real ends Unique, concordancy not set, one confidence-not-set end, one virtual end
Unique, concordant, Real ends Multiple, discordant, one unique end, one multiple end, not all non-prototype ends are ‘supporting’
Unique, concordant, Real ends Uniqueness-not-set, concordancy not set, one multiple end, one confidence-not-set end, not all non-prototype ends are ‘supporting’
Unique, concordant, Real ends Unique, concordant, unique ends, not all non-prototype ends are ‘supporting’
Clone with no end, no strand Clone with no end, no strand, unique, concordancy not set
Clone with no end, plus strand Clone with no end, plus strand, unique, concordant
Clone with no end, no strand, multiple, concordant not set Clone with no end, no strand, multiple, concordancy not set
Clone with no end, plus strand, discordant, unique not set Clone with no end, plus strand, discordant, unique not set

4. SNP Features

4.1 Color Code

Variation Type Color
Single Nucleotide Polymorphism Red
Deletion/Insertion Polymorphism Blue
Heterozygous Variation, undefined at nucleotide level Golden
Short Tandem Repeat (microsatellite) Polymorphism Yellow
Named Variation (insertion/deletion polymorphism of named repetitive element) Hunter Green
Sequence Scanned for Variation, but none observed Black
Mixed Variation (cluster contains submissions from 2 or more allelic classes) Green
MNP (multiple nucleotide polymorphism with alleles of common length > 1) Gray

4.1.1 Visual Examples

SNP insertion and deletion visual example

4.2 Shape Code

4.2.1 Weight indication

A SNP can be represented by either a hollow or a solid rectangle. A solid rectangle means that this particular SNP has a weight of 1, and a hollow rectangle indicates a weight of 2 or more.

Shape code

SNP Map weight info (the number of times a SNP maps to the genome contig (1-10))

1 hits genome once (on the same chromosome), annotated on NT_ contigs
2 hits genome twice, annotated on NT_ contigs with warning
3 hits genome 3-9 times, not annotated
10 hits 10+ times on genome, not annotated
(taken from SNP Documentation at http://www.ncbi.nlm.nih.gov/snp )

4.2.2 Insertion or deletion indication

To aid in distinguishing insertions and deletions, the blue SNP rectangles have additional markers:

4.2.2.1 Insertion

Insertions are marked with two hourglass-like triangles:

SNP insertion

4.2.2.2 Deletion

Deletions are marked with a triangle pointing downwards:

SNP deletion

4.3 SNP Bins For Clinical Associations

Color Description
Light Green No SNPs in this bin have an allele marked "Probable Pathogenic" or "Pathogenic"
Light Purple At least one SNP in this bin has an allele marked "Probable Pathogenic"; none are "Pathogenic"
Purple At least one SNP in this bin has an allele marked "Pathogenic"
SNP Bins

4.4 SNP Bins for Association Results

The color represents the highest p-value in that bin.

p-Value Range Color
< 2 Teal
2-3 Sky Blue
3-4 Blue
4-5 Green
5-6 Yellow
6-7 Orange
> 7 Red
The scatter plot above the bins reflects individual p-Values. Both the color (which uses the same coloring scheme) and the dot's location on the Y axis correspond to the p-Value.

SNP Bins for association results

5. Structural Variants

5.1 Common Rendering

There are four common scenarios for most variants (either SVs or SSVs) as shown in the table below. However, mixed cases with a defined breakpoint at one end and an undefined breakpoint range at the other end are possible as well. Here, we use (CNV SV) as examples:

Breakpoint Type Rendering Visual Example
With breakpoint resolution Fully saturated color With defined breakpoint range
With defined breakpoint range Transparent color for breakpoint ranges 5.1.2
With undefined breakpoint, but known outer bound Triangles pointing toward each other Defined breakpoint
With undefined breakpoint, but known inner bound Triangles pointing away from each other With defined breakpoint range

5.2 Variant Call Types (SSV) and Region Types (SV)

Type Comment Visual Example
Copy number variation

Color: violet

Four common cases, plus

CNV with length of deletion

(CNV)

5.2_1.png
Copy number gain or Duplication

Color: blue

(Gain SSV)

5.2_2.png
Copy number loss or Deletion

Color: red

The last one is a loss variant with length of deletion

(Loss SSV)

5.2_3.png
Mobile element insertion or Novel sequence insertion

Color: blue

(Insertion SV or SSV)

5.2_4.png
Tandem duplication

Color: deep brown

(Eversion SV or SSV)

5.2_5.png
Inversion

Color: light violet

(Inversion SV or SSV)

5.2_6.png
Translocation

Color: light indigo with pattern

(Translocation SV or SSV)

5.2_7.png
Complex

Color: light azure

(Complex SSV)

5.2_8.png
Insertion/Deletion or Indel Color: red Insert or delete indel
Unknown

Color: grey

(Unknown SV or SSV)

5.2_9.png
Note:

  1. SV region type “Copy number variation” can only have children of SSV Types “Copy number gain” and/or “Copy number loss” - in any combination. If all child SSV of a given SV are copy number gain or copy number loss, then the SV will be colored with the same way as the children are colored, blue for gain and red for loss, respectively. If the children are a mix of these two types, then the SV will be colored as violet.
  2. SV Type “Complex” can have either:

  3. children all of SSV Type “Complex,” or

  4. children of two or more SSV Types, in any combination (except “Copy number gain” and “Copy number loss,” which are covered above)

5.3. Rendering Styles for Linked Structural Variants Group

5.3.1 Default rendering with both parent and children shown

Default rendering example

5.3.2 Rendering with supporting variants in a packed form

If there are multiple types in the supporting variants, multiple colors will be used to reflect the corresponding allele type.

Rendering with supporting variants in a packed form Click and select the packed feature bar to show all the supporting variants.

Rendering with supporting variants

5.3.3 Superimpose all supporting variants over the parent variant

The supporting variants are superimposed on top of the parent variant with the shortest variants on the top. The colors reflect the corresponding allele type.

Superimpose all supporting variants over the parent variant

Click and select the packed feature bar to show all variants.

Expanded superimpose all supporting variants over the parent variant

5.4. Interactive Visualization of Variant Region Child Calls

Set Rendering options of the variation tab of the Configure dialog as "Show parent, Expand children upon a click".

Set rendering options

Sequence Viewer will show a plus sign with the number of child tracks for each parent track.

Parent track

Click on the plus sign, and Sequence Viewer will show all the child tracks and display the minus sign instead of plus at the parent track.

Expanded child tracks

Click on the minus sign to collapse the child tracks again.

6. Segmental Duplications

Identity Attribute Color Example
> 99.0 Orange Orange
> 98.0 Yellow ellow
> 90.0 Grey Grey
<= 90.0 Black Black

7. Alignments

Alignment tracks contain discrete sequences aligned pair-wise to the top-level assembly. These tracks are derived from sequence alignments reported in BAM or similar formats. NCBI BLAST results can also be visualized as alignments in the graphical sequence view.

7.1 Alignment Display

When the Alignment Display is set to “Adaptive” (default), alignment data is represented differently at different zoom levels (Figure 7.1.1). The Alignment Display can also be set to “Packed” (always shows the coverage or pile-up view), “Ladder” (one alignment per row) and “Show all” (always shows individual alignments). These options are found in the track display settings menu (Figure 7.3.1 and Table 7.3).

Zoom levels 7.1.1 Figure 7.1.1. View of alignments at different zoom levels when Alignment Display is set to “Adaptive”. At lower zoom levels, the alignments appear as a coverage or pile-up graphs in log 2 scale. At higher zoom levels, individual alignments become visible. Note that gaps and mismatches are colored in red.

At high zoom levels, alignment details become apparent. By default, matched bases and introns are colored in grey, mismatches and gaps are colored in red, and insertions are represented by blue bars (at higher zoom levels) or a blue hourglass with vertical blue bars proportional to the number of inserted bases (Figure 7.1.2). Less-than or greater-than signs (< or >) indicate the orientation of the alignment relative to the assembly.

Alignment features 7.1.2

Figure 7.1.2. Legend of alignment features.

7.2 Alignment Tooltips

Hovering the cursor over a discrete alignment reveals a tooltip that lists additional information about the alignment (Figure 7.2.1). Tooltips for alignment features report the coverage, identity, and number of mismatches, introns, and gaps in the alignment. If available/applicable, the CIGAR string is also provided. The coverage is calculated as the number of aligned bases divided by the total length of the feature sequence, while the identity is calculated as the number of matched bases divided by the aligned length (excluding gaps or introns, with no gap penalty). Unaligned nucleotides at the 5’ and 3’ ends are indicated and can be viewed by pressing the View button. Clicking on the magnifying glass on the top left of the tooltip resets the graphical view around the selected feature.

Tooltip reporting coverage 7.2.1 Figure 7.2.1. Tooltip for an alignment feature reporting coverage, identity, and number of mismatches, introns, and gaps. The lengths of 5’ and 3’ unaligned regions are reported, and pressing the view button reveals a window reporting a portion of the sequence with the unaligned residues colored in red.

7.3 Alignment Display Options

The track display settings can be accessed by clicking on the track title or selecting the “Configure Tracks” option under the “Tracks” button on the top right of the graphical viewer header. The track display settings menu (Figure 7.3.1) for alignment tracks provides a variety of different display and analysis options (Table 7.3). These options include, but are not limited to, creating a pile-up view, projecting features (Figure 7.3.5), and linking mate pairs (Figure 7.3.6). When the “Show pileup” option is selected, a pile-up view appears above the alignment (Figure 7.3.2). The Pileup Display dropdown menu includes options for the pile-up, including showing a match/mismatch graph (default view, Figure 7.3.2), match/mismatch table (Figure 7.3.3), or ATGC table (Figure 7.3.4). The Unaligned Tails dropdown menu includes options to show/hide unaligned tail lengths and unaligned sequences. For tracks where the metadata is available, users can also hide alignments (duplicates, bad reads) (Figure 7.3.7) or sort alignments.

Track display settings 7.3.1

Figure 7.3.1. Track display settings for alignment tracks.

Display Category Dropdown Menu Options
Alignment Display Adaptive
Packed
Ladder (one alignment per row)
Show all
Pileup Display Match/Mismatch graph (count)
Match/Mismatch graph (percentage)
ATGC graph (count)
ATGC graph (percentage)
Match/Mismatch table (count)
Match/Mismatch table (percentage)
ATGC table (count)
ATGC table (percentage)
Score method* Column Quality score DNA
Frequency-Based Difference
Show Differences
Nucleic Acid Colors
Quality Score
Disabled
Unaligned Tails Hide
Show Tail Length
Show Sequence
Hide alignments* None
Duplicates
Bad reads
Duplicates/Bad reads
Sort alignments by* No sorting
Alignment strand
Table 7.3. Alignment display options found in dropdown menus in the track display settings menu. *These options may not be comprehensive and may differ depending on the nature of the underlying track data.

Pile up graph 7.3.2 Figure 7.3.2. When the Pileup Display is set to “Match/Mismatch graph” (default), a pile-up graph displays above the alignments. Red markings in the graph denote mismatches while black markings denote gaps. Alignment display in figure is truncated.

Pile  up table 7.3.3 Figure 7.3.3. When the Pileup Display is set to “Match/Mismatch table (count)”, a pile-up table displays above the alignments. When zoom is set to sequence level, counts for intron, gap, mismatch, match, and total are reported for each position. A blank entry denotes a count of 0. Alignment display in figure is truncated.

ATGC table count 7.3.4 Figure 7.3.4. When the Pileup Display is set to “ATGC table (count)”, a pile-up table displays above the alignments. When zoom is set to sequence level, counts for total, A, T, G, C, gap, and intron are reported for each position. Each nucleotide is represented by a different color; the intensity of the color is correlated to the proportion of matches to that nucleotide at that position. A blank entry denotes a count of 0. Alignment display in figure is truncated.

RefSeqGene alignment feature 7.3.5 Figure 7.3.5. A RefSeqGene alignment feature (NG_029920.1) with the “Project features” option selected shows annotated RefSeq transcript (NM_), protein (NP_), and other features.

Sequence mate pairs 7.3.6 Figure 7.3.6. When the “Link Mate Pairs” option is selected, sequence mate pairs, if indicated by the metadata in the track, are linked by a dotted red line in the alignment display. When the “Show Labels” option is selected, labels for mate pairs are displayed.

PCR duplicates 7.3.7 Figure 7.3.7. PCR duplicates, if indicated by the metadata in the track, are colored in purple. PCR duplicates may also be reported in the feature tooltip. Duplicate alignments can be hidden from view by choosing “Duplicates” under the Hide alignments dropdown menu.

8. Sequence Track

The sequence track is represented by a solid bar at high zoom levels. Clicking on the zoom to sequence button (indicated by arrow below) changes the zoom level to show the sequence.

For nucleotide sequences, both the primary and complementary strands are shown. 5’ marks (circled in blue) at each end of the track indicate the strand orientation.

By default, the sequence track is located just below the ruler and the track label is hidden. The position of the track can be changed via drag and drop.

Sequence track

The track display setting for the sequence track is accessible in the track configuration panel and provides the option to show the label for this track.

Track display setting

8.1 Segment Color Code

For assembled sequences (e.g. genome assemblies), different types of sequence segments will be colored differently depending on the nature of the underlying component.

Segment Type Finished HTGS Draft HTGS WGS Other Gap
Color Blue Orange Green Grey Black

8.2 Restriction site map

Restriction enzyme recognition maps, for instance MAP_000012.1, can be viewed as sequence tracks with the restriction sites indicated by green triangles below the sequence bar.

View Visual Example
Zoomed-out view histogram
Zoomed-in view with tooltip popped up (if mouse hovering over the site) Smear Bar

9. Segment Map

Scaffolds (contigs) and tiling path (components) data tracks can be found under the Sequence vertical tab group in the track configuration panel.

9.1 Scaffolds

Scaffold Map Example

9.2 Tiling Path (Components)

Coloring of tiling path features follows the color scheme in Section 8.1 . Overlapping regions not in the path are colored in yellow.

Tiling Path (Component Map) Example

10. Six Frame Translations

Six Frame Translations

11. Label Placement

There are four global options regarding label placement: default, side label, top label, and no label. 'Default' may mean different settings for different objects. For example, default label placement for alignments is top labeling, but default setting for features is side labeling.

11.1 Side Label vs. Strand

In side labeling mode, the label is always placed at object's 5' side.

11.2 Examples

Label Placement Visual Example
Default Alignment (top):Top label placement
Component (inside):Inside label placement
Features (side):Side label placement
Side Label Side label
Top Label Top label
No Label No label

12. Histogram or Graph Rendering

Histogram or graph representation is used to visualize data that are distributed as data counts per position. This data is often in Wig, bigWig, or bedGraph format. Data types displayed as graphs include RNA-seq, epigenomic, and conservation data. Track display settings allow users to choose among display styles (Histogram, Heat Map, Line Graph) (Figure 12.1) and scale (Linear, Log Base 10, Log Base e, Log Base 2).

figure 12.1 graph display styles

Figure 12.1. Graph display styles.


By default, the value range of a histogram or line graph follows the local visible minimum and maximum values in the display. Zooming, panning, or otherwise changing the displayed region will cause the minimum and maximum values to adjust accordingly.

The user may select the “Set Value Range” option to manually control the value range in the display (Figure 12.2). This option is available when the display style is set to Histogram or Line Graph and the scale is set to Linear. If the data provider has stipulated minimum and maximum values for the track, the “Min value” and “Max value” fields will be pre-populated with these values. The user can apply pre-populated value ranges or customize the value range manually. If the track is part of a composite track group from a track hub, the option is available to apply the settings in bulk to all displayed tracks in the composite group.

Upon applying custom minimum and maximum values, any graph data that exceeds a set value range will be clipped in the display and colored in red to alert the user (Figure 12.3A). When the “Set Value Range” option is deselected, the value range will revert to use of the local minimum and maximum in the display (Figure 12.3B).

figure 12.2 graph track display settings dialog

Figure 12.2. Graph track display settings dialog.


figure 12.3 graph track with value range set

Figure 12.3. Graph track with value range set manually (A) or by default (B). (A) When the value range is set manually, any values exceeding the range are clipped and indicated in red. (B) When “Set Value Range” is deselected, the value range by default follows the local minimum and maximum values in the display.


12.1 Track Hubs: multiWig Tracks

Some track hubs include multiWig files, which are comprised of multiple subtracks. MultiWig files are shown in the graphical display as merged graphs with each subtrack in a different color (Figure 12.1.1). The track display settings for multiWig tracks provides options to adjust the scale and to display subtracks in a stacked format (Figure 12.1.2).

Clicking on the subtrack legend reveals a subtrack display settings dialog (Figure 12.1.3). Users can adjust the color, opacity, and display style of individual subtracks, which are listed in a drop-down menu. There is also an option to hide individual subtracks.

figure 12.1.1 merged versus stacked views

Figure 12.1.1. Merged versus Stacked views of multiWig files. Click on the legend to access subtrack display settings.


figure 12.1.2 multiwig track display settings dialog

Figure 12.1.2. MultiWig track display settings dialog.


figure 12.1.3 subtrack display settings dialog

Figure 12.1.3. Subtrack display settings dialog. The dropdown menu provides access to settings for all subtracks within the multiWig track.


13. Trace Graph Rendering

Rendering Options Visual Example
Default histogram
With confidence graph Smear Bar
Intensity bands Line Graph

Support Center

Last updated: 2019-05-13T16:19:03Z