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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 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

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