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Rice 50 genome browser |
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© 2013-2017 National Agriculture and Food Research Organization
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Rice 50 genome browser |
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© 2013-2017 National Agriculture and Food Research Organization
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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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Row1 |
Max: ▓ Min : ▓ |
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Row2 |
Max: ▓ Min : ▓ |
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Row3 |
Max: ▓ Min : ▓ |
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Row4 |
Max: ▓ Min : ▓ |
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| Criteria: | |
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| ID: | CDS region |
| Chromosome: | |
| Position: |
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* Maximum size is 20,000 bp |
| Quality: | >= |
| DP: | >= |
| Note: This tool has two functions. First is making an order of accessions sorted by genetic distance. Another one is making Phylogenetic tree (NJ) and downloading the tree (newick format). |
| Range of color gradient | Color definition for the color gradient | |
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SNP |
Max: ▓ Min : ▓ |
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INDEL |
Max: ▓ Min : ▓ |
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| DEPTH |
Max: ▓ Min : ▓ |
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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. |
| Targets: | : - |
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Flanking region(bp): |
* Maximum size is 10,000 bp |
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Avoiding primer design around target(bp): |
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| Quality: | >= |
| DP: | >= |
| Variant sites masking: | |
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Note: The sequence 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. |
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General settings
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| Product size range: | - |
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| Primer optimum size: | |
| Primer max size: | |
| Primer min size: | |
| Primer optimum TM: | |
| Primer max TM: | |
| Primer min TM: | |
| Max TM diffrence: | |
| Primer lowercase masking: |
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History
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Previous result is not found.
| Targets: | : - |
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Flanking region(bp):
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* Maximum size is 10,000 bp |
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Avoiding primer design around target(bp): |
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| Quality: | >= |
| DP: | >= |
| Variant sites masking: | |
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Note:
The sequence being exported with this option 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 above the threshold of depth and quality user set. |
| Chromosome: | |
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Position: |
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* Maximum size is 20,000 bp |
| Quality: | >= |
| DP: | >= |
| Line break (bp): | = |
| * Use 0 for non-breaking. | |
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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: | |
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Position: |
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* Maximum size is 200,000 bp |
| ID: | |
| Quality | >= |
| DP | >= |
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| Visible lists | Hidden lists | |||
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View ID or NAME Subtitle Width |
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Color Colors for each groups Destination group Color ▓ |
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| Keyword | ||
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* The keyword must has over 4 strings. |
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| Position | bp | |
| History |
| : Quality of Variant | |
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| : Depth of All reads | |
| : Depth of Alternative allele |
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Modes shown below can be changed at menu bar. |
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SNP only SNP frequency is shown by blue gradient. Regions with no mapped reads are highlighted with yellow. |
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DEPTH Average depth value of the block is shown by gray gradient. |
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Depth & SNP SNP frequency is shown in an inner box on depth background. |
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Drag Horizontally on the map. |
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Double click to zoom in around the clicked point. |
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Click on an accession name for changing the reference. Click again to restore the reference to the default setting. |
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| You will lose just all of your settings. (Data won't be deleted.) |
| * It will be reloaded when restore. |
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| * It will be reloaded. |
| : Number of blocks | |
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| : Block Height | |
| : Block Width |
This is the genome browser 'TASUKE version 1.5.0'.
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.
Questions or comments to
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 by gradational colors in a block whose size is variable from 1bp to 100kb.
Data constructionIllumina short reads of 50 rice re-sequencing data (1) was obtained from SRA. Preprocessing steps were as follows. Low quality bases were removed using fqcut and adapter sequences were trimmed using cutadapt (v1.0, 2). Reads were mapped to Nipponbare reference genome (IRGSP1.0, http://rapdb.dna.affrc.go.jp/download/irgsp1.html) by BWA (v0.6.1, 3) and Local Realignment was conducted using GATK (v1.6.5, 4). After removing PCR duplicated with Picard (v1.63, http://picard.sourceforge.net), variants were called by SAMtools (v0.1.18, 5). The effect of each variant site was annotated by using snpEff (6). Genes, repeat regions and SSR marker information in annotation tracks were obtained from RAP-DB (7, 8). Citation
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