NCBI中各个符号代表的意思

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NCBI User Document

1 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

Gene

RNA

Coding region

All other features

Color

Green

Blue

Red

Black

Visual Examples

1.2 Special Rendering Styles

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

1.2.1 Genes marked as pseudo

Settings

All features are

shown in one gene

group

Gene bar is hidden

Gene bar and gene

label are hidden

Visual Effect

Stripes over

green gene bar

Green stripe

background

Green stripe

background

Visual Examples

1.2.2 Features with exception text

Exception Example

Mismatch in

transcription

Mismatch for

translation

Unclassified

transcription

discrepancy

Visual Effect

Shaded

background

Shaded

background

Shaded

background

Visual Examples

1.2.3 Feature location marked as partial

Example

Partial start

Visual Effect

Black “<<” or “>>”

at 5’ end

Black “<<” or

“>>”at 3’ end

Visual Examples

Partial stop

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Partial start and stop

NCBI

Black “<<” and

“>>” at both ends

User Document

1.2.4 Features marked as partial

Example Cases

Example includes a partial

feature (marked as white

“<<” and “>>”) and

features with partial stop

(marked as black “>>”)

Visual Effect Visual Examples

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.

Décor

Styles

Default

Visual Effect

Solid bars for feature

intervals or exons, and

solid lines for introns

Arrows at both ends

showing the strand, and

lighten bars for introns

Visual Examples

Arrows

Square

anchor

Square for feature start,

arrow for feature stop,

dash lines for introns

Circle for feature start,

arrow for feature stop,

dash lines for 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

Circle

anchor

Fancy

Note: the glyphs representing feature start and stop will be rendered only when their sizes

can fit into the first and last intervals.

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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 CDS Features

When zoomed into the sequence level, both annotated protein sequence and translated

protein sequence are shown for CDS features.

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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 Clone Display

Display Description

Unique, concordant,

Real ends

Multiple,

concordant, Real

ends

Unique not Set,

Concordant, Real

ends

Unique, discordant,

Real ends

Multiple, discordant,

Real ends

Unique not set,

discordant, Real

ends

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Unique, Concordant

not set, Real ends

Multiple,

Concordant not set,

Real ends

Unique not set,

Concordant not set,

Real ends

Unique,

Concordant, One

virtual end

Multiple,

Concordant, One

virtual end

Unique not set,

Concordant, One

virtual end

Unique, Discordant,

One virtual end

Multiple, Discordant,

One virtual end

Unique not set,

Discordant, One

virtual end

Unique, Concordant

not set, One virtual

end

Multiple,

Concordant not set,

One virtual end

Unique not set,

Concordant not set,

One virtual end

Clone with no end,

no strand

Clone with no end,

plus strand

Clone with no end,

no strand, multiple,

concordant not set

Clone with no end,

plus strand,

discordant, unique

not set

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4 SNP Features

4.1 Color Code

Variation Type

Single Nucleotide Polymorphism

Deletion/Insertion Polymorphism

Heterozygous Variation, undefined at nucleotide level

Short Tandem Repeat (microsatellite) Polymorphism

Named Variation (insertion/deletion polymorphism of

named repetitive element)

Sequence Scanned for Variation, but none observed

Mixed Variation (cluster contains submissions from 2 or

more allelic classes)

MNP (multiple nucleotide polymorphism with alleles of

common length > 1)

4.1.1 Visual Examples

Color

Red

Blue

Golden

Yellow

Hunter Green

Black

Green

Gray

4.2 Shape Code

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))

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1

2

3

10

NCBI User Document

hits genome once (on the same chromosome),

annotated on NT_ contigs

hits genome twice, annotated on NT_ contigs with

warning

hits genome 3-9 times, not annotated

hits 10+ times on genome, not annotated

(taken from SNP documentation at

/snp )

4.3 SNP Bins For Clinical Associations

Color

Light Green

Description

No SNPs in this bin have an allele

marked “Probable Pathogenic” or

“Pathogenic”

At least one SNP in this bin has an

allele marked “Probable Pathogenic”;

none are “Pathogenic”

At least one SNP in this bin has an

allele marked “Pathogenic”

Light Purple

Purple

4.4 SNP Bins for Association Results

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

p-Value Range

<2

2-3

3-4

4-5

5-6

Color

Teal

Sky Blue

Blue

Green

Yellow

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6-7

>7

NCBI

Orange

Red

User Document

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

With breakpoint

resolution

With defined breakpoint

range

With undefined

breakpoint, but known

outer bound

With undefined

breakpoint, but known

inner bound

5.2 Variant Types

Variant

Type

Color Comment

Four common cases, plus

CNV with all insertion SSVs,

CNV with all Loss SSVs,

CNV with mixed SSVs

Other

Black

with

pattern

Four common cases

Visual Examples

Rendering

Fully saturated color

Transparent color for

breakpoint ranges

Triangles pointing

toward each other

Triangles pointing away

from each other

Visual Examples

CNV Black

5.3 Allele Types

Note: the first variant shown in all screenshots in this section is the parent variant (either

CNV SV or Other SV)

Allele Type

Variant

Type

Color Visual Examples

Gain CNV Blue

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Loss CNV

Red

Note: The last one is a

Loss variant with

allele_length

Complex

CNV/Other

Light azure

Unknown CNV Grey

Insertion CNV Tangerine yellow

Inversion Other Light violet with pattern

Loss of

Heterozygozity

Other Blue with pattern

Everted Other Deep brown with pattern

Uniparental

Disomy

Other Cyan with pattern

Translocation

Other Light indigo with pattern

5.4 Rendering Styles for Linked Structural Variants Group

5.4.1 Default rendering with both parent and children shown

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5.4.2 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.

5.4.3 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.

6 Segmental Duplications

Identity Attribute

> 99.0

> 98.0

> 90.0

<= 90.0

Color

Orange

Yellow

Grey

Black

Example

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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

Match

Mismatch

Gap

Insertion

Zoomed-out View

Grey bar

Red vertical bar

Red thin horizontal bar

Blue vertical bar

Zoomed-in View

Grey background

Red background

Red thin horizontal bar

Blue hourglass with a bar on both top and

bottom proportional to insertion bases

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7.3 Non-consensus splice site

NCBI User Document

7.4 Unaligned tails

The numbers above the box show the number of unaligned bases.

Unaligned Tail Type

PolyA

Other

7.5 Mate Pair Alignment

7.6 Multi-alignment

Visual Examples

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.

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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

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

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.

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

Color

9.2 Scaffold Map Example

Finished

Blue

Draft

Orange

WGS

Green

Other

Grey

Gap

Black

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9.3 Tiling Path (Component Map) Example

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.

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11.2 Examples

Label Placement

NCBI User Document

Visual Examples

Alignment (top):

Default

Component (inside):

Features (side):

Side Label

Top Label

No Label

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