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 covers features that use generic feature rendering settings. The features (SNPs, structural variants, clone placements, and segmental duplications) that require special handling are covered in the later sections.

1.1 Feature Color Code

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

1.2 Special Rendering Styles

For features with special attributes, special rendering will be applied.

1.2.1 Genes marked as pseudo

Settings	Visual Effect	Visual Examples
All features are shown in one gene group	Stripes over green gene bar
Gene bar is hidden	Green stripe background
Gene bar and gene label are hidden	Green stripe background

1.2.2 Features with exception text

Exception Example	Visual Effect	Visual Examples
exception on RNA or CDS feature	Shaded background

1.2.3 Feature location marked as partial

Settings	Visual Effect	Visual Examples
Partial Start	Black "<<" or ">>" at 5' end
Partial Stop	Black "<<" or ">>" at 3' end
Partial start and stop for internal fuzz on mRNAs/CDSs	Black “<<” and “>>” at both ends
Partial Start and Stop	Black "<<" and ">>" at both ends

1.2.4 Features marked as partial

Example Cases	Visual Effect	Visual Examples
Example includes a partial feature (marked as white "<<" and ">>") and features with partial stop (marked as black ">>")	White "<<" and ">>" at both ends

1.3 Feature Decorations

Different feature decoration styles are solely for offering different ways of visualization. The exact same feature can be rendered using each of the five existing styles.

Decor Style	Visual Effect	Visual Examples
Default	Solid bars for feature intervals or exons, and solid lines for introns
Arrows	Arrows at both ends showing the strand, and lighten bars for introns
Square Anchor	Square for feature start, arrow for feature stop, dash lines for introns
Circle Anchor	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, lighten bars for mRNA introns, and canted lines for CDS introns

Note: the glyphs representing feature start and stop will be rendered only when their sizes can fit into the first and last intervals.

2. Gene Model Features

A Gene Model is a feature group that contains four main features: gene, mRNA, CDS and Exon. The group may also contain SNP and other features that are projected from mRNA and CDS products.

2.1 Gene Model Rendering

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

Rendering for insertions and deletions

2.3 Feature Ruler

For a selected RNA or CDS feature, a feature ruler will be show with the feature's local coordinate.

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
	Insert only	Single arrow
	Combined end-seq and insert	2 arrows joined by line or single arrow on yellow background
Concordancy	Concordant	Color: Blue
	Discordant	Color: Red
	Concordancy not set	Color: Gray
End-seq only clone placement uniqueness	Unique	Connecting Line: solid
	Multiple	Connecting Line: dotted
	Uniqueness not set	Connecting line: dashed
Clone end confidence	Unique	Fill: solid color
	Multiple	Fill: vertical bars
	Virtual	Fill: empty
	Other/Not set	Fill: horizontal bars
Insert only clone placement uniqueness	Unique	Fill: solid color
	Multiple	Fill: vertical bars
	Other/not set	Fill: horizontal bars
Directionality	Forward or Backward	Arrow
Supporting Evidence	All non-prototype ends are ‘supporting’	With no shaded background
	Not all non-prototype ends are ‘supporting’	With shaded background

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

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.

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:

4.2.2.2 Deletion

Deletions are marked with a triangle pointing downwards:

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"

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.

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	Transparent color for breakpoint ranges
With undefined breakpoint, but known outer bound	Triangles pointing toward each other
With undefined breakpoint, but known inner bound	Triangles pointing away from each other

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)
Copy number gain or Duplication	Color: blue (Gain SSV)
Copy number loss or Deletion	Color: red The last one is a loss variant with length of deletion (Loss SSV)
Mobile element insertion or Novel sequence insertion	Color: blue (Insertion SV or SSV)
Tandem duplication	Color: deep brown (Eversion SV or SSV)
Inversion	Color: light violet (Inversion SV or SSV)
Translocation	Color: light indigo with pattern (Translocation SV or SSV)
Complex	Color: light azure (Complex SSV)
Insertion/Deletion or Indel	Color: red
Unknown	Color: grey (Unknown SV or SSV)

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

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.

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

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

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".

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

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

6. Segmental Duplications

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

7. Alignments

7.1 Alignment in Different Mode

7.1.1 With Score Coloration Disabled

7.1.2 With Score Coloration Enabled

7.2 Alignment Score Coloration

There are four possible aligned-types: match, mismatch, gap (deletion), and insertion. The visual representations for all four different glyphs are illustrated in the table blow, and as well as in the screenshots.

Align-type	Zoomed-out View	Zoomed-in View
Match	Grey bar	Grey background
Mismatch	Red vertical bar	Red background
Gap	Red thin horizontal bar	Red thin horizontal bar
Insertion	Blue vertical bar	Blue hourglass with a bar on both top and bottom proportional to insertion bases

7.3 Non-consensus splice site

7.4 Unaligned regions

7.4.1 Unaligned tails

The numbers on the side of the box show the number of unaligned bases.

Unaligned Tail Type	Visual Examples
PolyA
Other

Display Option	Visual Examples
Hide tails
Show tail length
Show tail sequence

The unaligned sequence is displayed with pink background.

7.4.2 Internal unaligned regions

The internal unaligned region is rendered with dashed line, showing the number of unaligned bases.

Visual Example

7.5 Mate Pair Alignment

Display Option	value	Description	Default
LinkMatePairAligns	true/false	The option clusters the mate-pair reads and connects them with a dotted line	false

7.6 Multi-alignment

7.7 Smeared Alignment

7.8 Alignment statistics

This option displays statistics at a given base position across all related alignments that have coverage at that base. The statistics include individual counts for A, G, T, C and Gap. Several other statistics can be derived with a known reference sequence base, including: matches, mismatches and total alignment count. There are eight different combinations of rendering with these three settings: Content (A/T/G/C/Gaps or Matches/Mismatches/Gaps), Data type (Count or Percentage), and Display (Bar graph or Smear table). Here are several examples.

7.8.1 Zoomed-out view of a bar graph with match/mismatch/gap count

7.8.2 Zoomed-in view of a smear table with A/G/T/C/Gap count

7.8.3 Zoomed-in view of a bar graph with A/G/T/C/Gap count

7.9 PCR duplicates and failed chastity reads

Deep-targeted sequencing data can contain PCR duplicates, inflating perceived read depth.

Data can also contain failed chastity reads.

7.9.1 PCR duplicates

7.9.2 Failed chastity reads

8. Sequence Track

The grey bar represents the sequence track in zoomed-out view

In zoomed-in view, both original sequence (top) and the complementary sequence (bottom) are shown.

8.1 Restriction sites

Each restriction site is shown as a green triangle right below the gray sequence bar at the corresponding site position. Sample molecule: MAP_000012.1

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

8.2 Restriction sites on feature tracks

Each restriction site's interval is displayed as a bar (with strand indication) . Each cut point is displayed as a marker (triangle). The cut markers are hidden if too small (depending on the zoom level). When the restriction site is selected, the location of the cut points is indicated with a "hairline".

View	Visual Example
Restriction site (zoomed in)
Restriction site (selected, zoomed in)
Restriction site (selected, zoomed out)

9. Segment Map

Depending on the sequence type, a sequence may have scaffold (contig) map, and/or tiling path (component map).

9.1 Segment Color Code

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

9.2 Scaffold Map Example

9.3 Tiling Path (Component Map) Example

If the map has only grey segments without overlap shown as in previous picture it can mean the zoom level is too low and the map contains too many segments. Try to zoom in to get more detailed picture.

10. 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):
	Component (inside):
	Features (side):
Side Label
Top Label
No Label

12. Histogram or Graph Rendering

Histogram or Graph representation is used to visualize feature density map at a zoomed-out view or coverage graph data that are one value per base or multiple bases. There are three different types of rendering styles: histogram, smear bar and line graph. Please note: both the color and graph height are configurable.

Rendering Style	Visual Example
Histogram
Smear Bar
Line Graph

Some Histograms or Line Graphs have a high dynamic range that makes the data hard to interpret. To make sense of these, outliers can be expressed in terms of standard deviation of the data and, if clipping is on, removed from the data and rendered in a different color (default – red).

Scale	Visual Example
Linear
Linear with outlier clipping
Logarithmic

13. Trace Graph Rendering

Rendering Options	Visual Example
Default
With confidence graph
Intensity bands

Table of Contents

• Sequence Viewer application
• Documentation Home
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