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Condition:
is viewed as general purpose data.
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Conditions Color definition Preview of the block
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  BLAST
- BLAST Tutrial
- About using tools
Query: Enter FASTA sequence
Alignment Options
General Parameters
Max target sequences:
E-value:  
Word size:  
Max matches in a query range:  
Scoring Parameters
Match/Mismatch Scores:
Gap Costs:
History

Previous result is not found.



  Phylogenetic tree
- Phylogenetic Tree Tutrial
- About using tools
Select Accessions:
Hide
Show
Select Region:
Gene ID:    CDS region
Chromosome:  
Position:    -    
* Maximum size is 20,000 bp
Quality: >=  
DEPTH: >=  

OS01t0100100-01 Phylogenetic Analysis
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.
  Primer designing
  • Run Primer3
  • Exporting sequence
- Primer designing Tutrial
- 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:
YES NO
Note: Variant sites (regardless "hetero" or "homo") passing thresholds set below will be masked as "N" in the input sequence.
Quality: ≧  
DEPTH: ≧  
Avoid sites with
"Depth=NA":
NO Yes
Ratio of "DEPTH = NA" accessions : 
Number of "DEPTH = NA" accessions : 
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:
YES NO
Note: Variant sites (regardless "hetero" or "homo") passing thresholds set below will be masked as "N" in the input sequence.
Quality: ≧ 
DEPTH: ≧ 

Chromosome:
Position:
  		 -    
* Maximum size is 20,000 bp
Quality: >=  
DEPTH: >=  
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.

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

  • Accession lists



  • Accession title

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

  • Recovery lists (original)

    •   Search
    Keyword  
    (eg. Os01g0100100-01) * 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.
    You will lose just all of your settings.
    (Data won't be deleted.)
    * It will be reloaded when restore.

    * It will be reloaded.
    : Number of blocks
    : Block Height
    : Block Width

  • ▓ MODIFIER
    • INTERGENIC
    • UPSTREAM
    • DOWNSTREAM
    • UTR_5_PRIME
    • UTR_3_PRIME
    • REGULATION
    • INTRAGENIC
    • GENE
    • INTRON_CONSERVED
    • INTRON
    • INTERGENIC_CONSERVED
  • ▓ LOW
    • SYNONYMOUS_START
    • NON_SYNONYMOUS_START
    • START_GAINED
    • SYNONYMOUS_CODING
    • SYNONYMOUS_STOP
    • EXON
    • 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

    • What is snpEff?
      GWAS
    phenotype selection
    Filter By snpEff Impact level
        HIGH
             
        MODERATE
              ;         
        LOW
           
        MODIFIER
                       NONE
    Sort ByPositionProbability