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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

Query: | Enter FASTA sequence

Alignment Options

General Parameters

Program: |
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

Select Accessions: |
Display mode: Use sorting SystemTree order(Don't use sorting) * Check/Uncheck accessions, then submit using the “Run” button in the bottom. Only checked ones will be used for analysis. * Use filtering, sorting, and row selection to refine accessions and toggle them in bulk via "Action". Action: Columns to display:
Target accessions: | All: Filtering: Checking:
MoveTo & Select Acc:
Hide
Show

Select Region:
Feature ID: CDS region
Chromosome:
Position: -
* Maximum size is 20,000 bp
Calc-Method:

Based on DNA sequence. For long sequence, the analysis takes a long time. It preferentially outputs variant type (ALT) allele. INS/DEL-gap alignment regions are removed. If GT is "0/1", outputs ambiguous base(IUPAC) of REF and ALT. (ex. C/T = Y) If GT is "1/2"(hetero without REF), outputs ambiguous base of two ALT alleles. Based on presence or absence of variants. Target variant types: SNP INS DEL

Variant Filter: Quality: >=
DEPTH: >=
Note: If the tree is not displayed correctly, please change the sample "Name" to "ID" in AccessionManager.

OS01t0100100-01 Phylogenetic Analysis

| 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

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: Sets the quality threshold for variant sites ("hetero" or "homo"). Those sites are masked as "N".
| Quality: ≧
| DEPTH: ≧
Avoid sites with "Depth=NA": | NO Yes
| Allowed ratio of "DEPTH = NA" accessions : ≤
| Allowed 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: ≧

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.

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

Leaves number
* If it can not collapse to specified number, it collapses to a close number.

### Accession list
Display mode: Use sorting SystemTree order(Don't use sorting) Action: Columns to display:
| Target accessions: | All: Filtering: Checking:
MoveTo & Select Acc: |  |
Hide
Show
* Since SystemTree is ON, the above sort order is not reflected in track.

### 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) |

Search

Keyword |
| (eg. Os01g0100100-01) * The keyword must have at least 3 characters. |
Position |
ID/Name |
History |

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

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.

Keyword:

You will lose just all of your settings. (Data won't be deleted.)
* It will be reloaded when restore.

ID | NAME | VARIETY | SUB VARIETY | ORIGIN | ORIGIN2 | TYPE | OTHER1 | OTRER2 |
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---

* It will be reloaded.

| : Number of blocks
| : Block Height
| : Block Width

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?
GWAS

| Select phenotype

Select chromosome |

Filter by SnpEff Impact level (combine with "OR")
HIGH MODERATE LOW MODIFIER NONE

Sort by Position Probability