Condition:	is viewed as general purpose data.
[]

View multiple conditions:

Conditions	Color definition	Preview of the block
Row1	Max: ▓ Min : ▓
Row2	Max: ▓ Min : ▓
Row3	Max: ▓ Min : ▓
Row4	Max: ▓ Min : ▓

Criteria:
ID:	CDS region

Chromosome:
Position:	- * Maximum size is 20,000 bp

Quality:	>=
DP:	>=
	Note: This tool has two functions. First is making an order of accessions sorted by genetic distance. Another one is making Phylogenetic tree (NJ) and downloading the tree (newick format).

	Range of color gradient	Color definition for the color gradient
SNP		Max: ▓ Min : ▓
INDEL		Max: ▓ Min : ▓
DEPTH		Max: ▓ Min : ▓
		Max: ▓ Min : ▓

Range of color gradient

Color definition for the color gradient

SNP

Max: ▓

Min : ▓

INDEL

Max: ▓

Min : ▓

DEPTH

Max: ▓

Min : ▓

Max: ▓

Min : ▓

Note: These settings will be applied every block size. When SNP or INDEL minimum value are less than 1, these will be rounded up the value to 1.

Run Primer3
Exporting sequence

Targets:	: -
Flanking region(bp):	* Maximum size is 10,000 bp

Avoiding primer design around target(bp):
Quality:	>=
DP:	>=
Variant sites masking:
	Note: The sequence shows preferentially variant type allele regardless of its genotype "heterozygous or homozygous". Ns in the alignment indicates unmapped site (Depth = 0) as well as site below the threshold of depth and quality user set.
General settings

Product size range:	-
Primer optimum size:
Primer max size:
Primer min size:
Primer optimum TM:
Primer max TM:
Primer min TM:
Max TM diffrence:
Primer lowercase masking:

History

Previous result is not found.

Targets:	: -
Flanking region(bp):	* Maximum size is 10,000 bp

Avoiding primer design around target(bp):
Quality:	>=
DP:	>=
Variant sites masking:
	Note: The sequence being exported with this option shows preferentially variant type allele regardless of its genotype "heterozygous or homozygous". Ns in the alignment indicates unmapped site (Depth = 0) as well as site above the threshold of depth and quality user set.

Chromosome:
Position:	- * Maximum size is 20,000 bp

Quality:	>=
DP:	>=
Line break (bp):	=
	* Use 0 for non-breaking.
	Note: The fasta file being exported shows preferentially variant type allele regardless of its genotype "heterozygous or homozygous". Ns in the alignment indicates unmapped site (Depth = 0) as well as site below the threshold of depth and quality user set.

Accession lists

Visible lists

Hidden lists

Accession title
View ID or NAME Subtitle Width
Color Colors for each groups Destination group Color ▓

Recovery lists (original)

Keyword
	* The keyword must have at least 4 characters.
Position	bp
History

	: Quality of Variant
	: Depth of All reads
	: Depth of Alternative allele

To learn more about how to use TASUKE, visit this page.

Display Modes Modes shown below can be changed at menu bar.
	SNP only SNP frequency is shown by blue gradient. Regions with no mapped reads are highlighted with yellow.
	DEPTH Average depth value of the block is shown by gray gradient.
	Depth & SNP SNP frequency is shown in an inner box on depth background.

Mouse
	Drag Horizontally on the map.
	Double click to zoom in around the clicked point.
	Click on an accession name for changing the reference. Click again to restore the reference to the default setting.

Shortcut keys

Movements
←	Moving to the left side window.
→	Moving to the right side window.
<space>	Moving to the right side window.
<home>	Moving to the head of current chr.
<end>	Moving to the tail of current chr.
↑	Zoom in.
<+>	Zoom in.
<->	Zoom out.
↓	Zoom out.

Display modes
p	DEPTH only
s	SNP only
i	INDEL only
a	SNP and INDEL
d	Show/Hide indicator on map.
n	Show/Hide DEPTH=0
e	On/Off snpEff
b	On/Off Snpblock
h	This manual page.

	: Number of blocks
	: Block Height
	: Block Width

▓ LEVEL 0

INTERGENIC

▓ LEVEL 1

UPSTREAM
DOWNSTREAM

▓ LEVEL 2

UTR_5_PRIME
UTR_3_PRIME
REGULATION
INTRAGENIC
GENE
INTRON_CONSERVED
INTRON
INTERGENIC_CONSERVED

▓ LEVEL 3

SYNONYMOUS_START
NON_SYNONYMOUS_START
START_GAINED
SYNONYMOUS_CODING
SYNONYMOUS_STOP
EXON
CDS
TRANSCRIPT

▓ LEVEL 4

NON_SYNONYMOUS_CODING
CODON_CHANGE
CODON_INSERTION
CODON_CHANGE_PLUS_CODON_INSERTION
CODON_DELETION
CODON_CHANGE_PLUS_CODON_DELETION
UTR_5_DELETED
UTR_3_DELETED

▓ LEVEL 5

SPLICE_SITE_ACCEPTOR
SPLICE_SITE_DONOR
START_LOST
EXON_DELETED
FRAME_SHIFT
STOP_GAINED
STOP_LOST
RARE_AMINO_ACID

What is snpEff?

Version

This is the genome browser 'TASUKE version 1.5.2'.

Contact

Questions or comments to

General description

This browser shows genome wide variant and coverage depth of re-sequencing data as well as annotation information such as genes, repeats, markers and the rest. Number of variants and depth of coverage are shown by gradational colors in a block whose size is variable from 1bp to 100kb. For more information, please see the TASUKE website.

Chromosome:
Position:	- * Maximum size is 200,000 bp
ID:
Quality	>=

DP	>=

Accession lists

Accession title

Recovery lists (original)

Version

Contact

General description