Loading...

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

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 Tutorial
- About using tools

Select Accessions: |
Hide
Show
Select Region: |
| Gene ID: CDS region
| Chromosome:
| Position: - * Maximum size is 20,000 bp
Variant Filter: | Quality: >=
| DEPTH: >=
| Note: It preferentially outputs variant type (ALT) allele regardless of its genotype "heterozygous or homozygous". If GT is "1/2"(hetero without REF), the left side of the two alleles separated by comma is used.

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

- 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: | YES NO
| Note: Variant sites ("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
| 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

Chromosome: |
Position: | - * Maximum size is 200,000 bp
Variant Filer: | 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". If GT is "1/2"(hetero without REF), the left side of the two alleles separated by comma is output. 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: |
Variant Filter: | Quality: >=
| DEPTH: >=

### Accession list

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

### Recovery list (original)

Search

Keyword |
| (eg. Os01g0100100-01) * The keyword must have at least 4 characters. |
Position |
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.
| SNP only SNP frequency is shown in blue gradient. Regions with no mapped reads are highlighted in yellow.
| DEPTH Average depth value of the block is shown in gray gradient.
| Depth & SNP SNP frequency 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
b | On/Off Snpblock
h | This manual page.

Keyword:

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

EFF ANN
- ▓ 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
- ▓ 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
HIGH MODERATE LOW MODIFIER NONE

Sort by Position Probability