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Human 100 genome browser |
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© 2013-2017 National Agriculture and Food Research Organization
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Human 100 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 constructionWe constructed Tasuke data base for 100 human genomes consisting low coverage resequencing data from 1000 genomes project (ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/). Alignment files of arbitrarily selected 100 individuals representing 19 subpopulations were downloaded. The alignments were generated by mapping illumina short reads to human reference genome (GRCh37 build, http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/). Variants were called by using SAMtools (v0.1.18, 1). The effect of each variant site was annotated by using snpEff (2). Annotation information was obtained from Ensembl (3). Citation
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