TASUKE+ for RAP-DB

Genome-wide variations for 685 rice varieties

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 : ▓

BLAST

- BLAST Tutorial

- About using tools

Query:	Enter FASTA sequence

Alignment Options

Match/Mismatch Scores:
Gap Costs:

History


        
        

        Previous result is not found.

Phylogenetic Tree

- Phylogenetic Tree Tutorial

- About using tools

Select Accessions:

MoveTo & Select Acc:

Hide

Show

Select Region:

Feature ID: CDS region

Chromosome:

Position: -
* Maximum size is 20,000 bp

Variant Filter:

Quality: >=

DEPTH: >=

Note: It preferentially outputs variant type (ALT) allele. DEL-gap alignment regions are removed.
If GT is "0/1", outputs ambiguous base(IUPAC) of REF and ALT. (SNP only. ex. C/T = Y)
If GT is "1/2"(hetero without REF), outputs ambiguous base of two ALT alleles. (SNP/SNP only)
If the tree is not displayed correctly, please change the sample "Name" to "ID" in AccessionManager.

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

Range of color gradient

Color definition

SNP

Max: ▓

Min : ▓

INDEL

Max: ▓

Min : ▓

DEPTH

Max: ▓

Min : ▓

Max: ▓

Min : ▓

Note: The selected settings are applied to each block. If the minimum SNP and INDEL value is >1, the value is rounded-up to 1.

Primer design

Run Primer3
Exporting sequence

- Primer design Tutorial

- About using tools

Settings

Target

: -

* Maximum size of target + flanking region is 50,000 bp

Flanking region (bp)

* Maximum size of target + flanking region is 50,000 bp

Avoid sites around
the target (bp)

Variant sites masking

Note: Sets the quality threshold for variant sites ("hetero" or "homo"). Those sites are masked as "N".

Quality

: ≧

DEPTH

: ≧

Avoid sites with
"Depth=NA":

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:

e-PCR	ON OFF

	Product size range : -
	Primer max TM :
	Primer min TM :
	Concentration of monovalent cations :
	Concentration of divalent cations :
	Concentration of dNTPs(mM) :
	Annealing oligo concentration(nM) :

History

Previous result is not found.

Target

: -

Flanking region (bp)

* Maximum size of target + flanking region is 50,000 bp

Avoid sites around
the target (bp)

Variant sites masking

Note: Variant sites (regardless "hetero" or "homo") passing thresholds set below will be masked as "N" in the input sequence.

Quality

: ≧

DEPTH

: ≧

Exporting FASTA

Select Region:
	Feature ID: export as

	Chromosome:
	Position: - * Maximum size is 200,000 bp

	Reverse complement
Variant Filer:	Quality: >=
	DEPTH: >=
	Replace excluded(low quality) variants with "N" (default: reference-seq)
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". All Accession sequences(DNA) are aligned by gaps and have the same length. Ns in the alignment indicates unmapped site (Depth=0). If GT is "1/2"(hetero without REF), the first ALT allele is output.

Accession list

MoveTo & Select Acc:

Hide

Show

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

System tree (Whole genome tree)

* SystemTree is not used.

Style: Type Correction Sort by

View: Width

Threshold of auto node collapsing:
Comparison with TreeHeight: ***

Recovery list (original)

To learn more about using TASUKE, visit this page.

Display Modes Modes shown below can be changed at menu bar. There are two modes for displaying variant: "block" unit and "one-base" unit. The "block" mode has two variant color modes: "Frequency" and "SnpEff". The "one-base" mode has three color modes: "Allele", "GT", and "SnpEff".
	Variant only. "Block" is shown variant frequency in blue gradation. In "one-base", each variant is displayed as a bar. Regions with no mapped reads are highlighted in yellow.
	DEPTH. Average depth value of the block is shown in gray gradient.
	Depth & Varaint. Variant is shown as inner box with the depth as 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
←	Move to left window
→	Move to right window
<space>	Move to right window
<home>	Move to head of current chr
<end>	Move to tail of current chr
↑	Zoom in
<+>	Zoom in
<->	Zoom out
↓	Zoom out

Display modes
p	Show/Hide DEPTH
s	Show/Hide SNP
i	Show/Hide INDEL
d	Show/Hide indicator on map
n	Show/Hide DEPTH=0
e	On/Off SnpEff
r	On/Off SystemTree
b	On/Off Block mode
l	On/Off Cursor lines
h	This manual page.

EFF ANN

▓ MODIFIER

INTERGENIC
UPSTREAM
DOWNSTREAM
UTR_5_PRIME
UTR_3_PRIME
REGULATION
INTRAGENIC
EXON
GENE
INTRON_CONSERVED
INTRON
INTERGENIC_CONSERVED

▓ LOW

SYNONYMOUS_START
NON_SYNONYMOUS_START
START_GAINED
SYNONYMOUS_CODING
SYNONYMOUS_STOP
CDS
TRANSCRIPT
CHROMOSOME_LARGE_DUPLICATION
SPLICE_SITE_REGION
SPLICE_SITE_BRANCH
SPLICE_SITE_BRANCH_U12
MICRO_RNA
NON_SYNONYMOUS_STOP

▓ MODERATE

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
CHROMOSOME_LARGE_INVERSION
NEXT_PROT

▓ HIGH

SPLICE_SITE_ACCEPTOR
SPLICE_SITE_DONOR
START_LOST
EXON_DELETED
FRAME_SHIFT
STOP_GAINED
STOP_LOST
RARE_AMINO_ACID
CHROMOSOME_LARGEDELETION
EXON_DELETED_PARTIAL
EXON_DUPLICATION
EXON_DUPLICATION_PARTIAL
EXON_INVERSION
EXON_INVERSION_PARTIAL
GENE_DELETED
GENE_DUPLICATION
GENE_FUSION
GENE_FUSION_HALF
GENE_FUSION_REVERESE
GENE_REARRANGEMENT
PROTEIN_PROTEIN_INTERACTION_LOCUS
PROTEIN_STRUCTURAL_INTERACTION_LOCUS
TRANSCRIPT_DELETE

▓ MODIFIER

intergenic_region
upstream_gene_variant
downstream_gene_variant
5_prime_utr_variant
3_prime_utr_variant
regulatory_region_variant
intragenic_variant
gene_variant
exon_variant
conserved_intron_variant
intron_variant
conserved_intergenic_variant
coding_sequence_variant
miRNA
non_coding_transcript_exon_variant
non_coding_transcript_variant
transcript_variant
sequence_feature

▓ LOW

start_retained
initiator_codon_variant
synonymous_variant
stop_retained_variant
splice_region_variant
5_prime_UTR_prematurestart_codon_gain_variant
5_prime_UTR_premature_start_codon_gain_variant
start_codon_gain_variant

▓ MODERATE

missense_variant
inframe_insertion
inframe_deletion
disruptive_inframe_insertion
disruptive_inframe_deletion
5_prime_utr_truncation
3_prime_utr_truncation

▓ HIGH

splice_acceptor_variant
splice_donor_variant
start_lost
exon_loss_variant
frameshift_variant
stop_gained
stop_lost
rare_amino_acid_variant
duplication
inversion
feature_ablation
gene_fusion
bidirectional_gene_fusion
rearranged_at_DNA_level
protein_protein_contact
structural_interaction_variant
chromosome

What is SnpEff?

Version

This is the genome browser TASUKE+ Version .

Kumagai M, Nishikawa D, Kawahara Y, Wakimoto H, Itoh R, Tabei N, Tanaka T, Itoh T. (2019) TASUKE+: a web-based platform for exploring GWAS results and large-scale resequencing data. DNA Research, 2019, 26(6), 445-452.

Kumagai M., Kim J., Itoh R. and Itoh T. (2013) TASUKE: a web-based visualization program for large-scale resequencing data. Bioinformatics. 29 (14): 1806-1808.

Contact

Questions or comments

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 in blocks with color gradiation and size varying in size from 1bp to 100 kb. The browser also shows the input data in a GWAS plot.

PRIMER

using tool

primer3-2.3.7+

official site

http://primer3.sourceforge.net/

Reference

Andreas Untergasser,Ioana Cutcutache,Triinu Koressaar,

Jian Ye,Brant C. Faircloth,Maido Remm,Steven G. Rozen

Primer3-new capabilities and interfaces

Nucleic Acids Res (2012) 40 (15): e115.

https://academic.oup.com/nar/article/40/15/e115/1223759/Primer3-new-capabilities-and-interfaces

ePCR

using tool

MFEprimer-3.0+

TASUKE+ supports both MFEprimer-2 and MFEprimer-3.

official site

https://www.mfeprimer.com/

Reference

Kun Wang, Haiwei Li, Yue Xu, Qianzhi Shao, Jianming Yi, Ruichao Wang,

Wanshi Cai, Xingyi Hang, Chenggang Zhang, Haoyang Cai, Wubin Qu

MFEprimer-3.0: quality control for PCR primers.

Nucleic Acids Res (2019) 47(W1): W610-W613

https://academic.oup.com/nar/article/47/W1/W610/5486745

BLAST

using tool

ncbi-blast-2.6.0+

official site

https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download

Reference

Christiam Camacho, George Coulouris, Vahram Avagyan,

Ning Ma, Jason Papadopoulos, Kevin Bealer and Thomas L Madden

BLAST+: architecture and applications

BMC Bioinformatics200910:421

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105 -10-421

PHYLOGENETIC TREE

using tool

dnadist, neighbor, retree(PHYLIP version 3.695)

official site

https://phylipweb.github.io/phylip/

Program:

Max target sequences:

E-value:

Word size:

Max matches in a query range:

	: Quality of variant
	: Depth of all reads
	: Depth of alternative allele
SnpEff Variant impact: HIGH MODERATE LOW MODIFIER NONE

Accession list

Accession title

System tree (Whole genome tree)

Recovery list (original)

Version

Contact

General description

PRIMER

using tool

official site

Reference

ePCR

using tool

official site

Reference

BLAST

using tool

official site

Reference

PHYLOGENETIC TREE

using tool

official site

Data construction

Citation

Chromosome:
Position:	- * Maximum size is 200,000 bp
Feature ID:

Variant Filter:	Quality: >=

	DEPTH: >=