Chromosome:
Position:	- * Maximum size is 10,000 bp

Quality:	>=
DP:	>=
Line Width:	=
	* Use 0 for single line out.
	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	>=
DP	>=

Accession lists

Visible lists

Hidden lists

Accession title
ID or NAME Subtitle Width

Recovery lists (original)

ID
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

□ LEVEL 0

INTERGENIC

▓ LEVEL 1

UPSTREAM
DOWNSTREAM

▓ LEVEL 2

UTR_5_PRIME
UTR_3_PRIME
REGULATION
INTRAGENIC
GENE
INTRON_CONSERVED
INTRON
INTERGENIC_CONSERVED

▓ LEVEL 3

SYNONYMOUS_START
NON_SYNONYMOUS_START
START_GAINED
SYNONYMOUS_CODING
SYNONYMOUS_STOP
EXON
CDS
TRANSCRIPT

▓ LEVEL 4

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

▓ LEVEL 5

SPLICE_SITE_ACCEPTOR
SPLICE_SITE_DONOR
START_LOST
EXON_DELETED
FRAME_SHIFT
STOP_GAINED
STOP_LOST
RARE_AMINO_ACID

What is snpEff?

Version

This is the genome browser 'TASUKE'.

Contact

Questions or comments to here

General description

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 construction

Illumina short reads of 50 rice re-sequencing data (1) were obtained from SRA. Low quality bases were removed using fqcut and adapter sequences were trimmed using cutadapt (v1.0, 2). Processed reads were mapped to Kasalath pseudomolecule by BWA (v0.6.2, 3) and Local Realignment was conducted using GATK (v1.6.5, 4). After removing PCR duplicates with Picard (v1.92, http://picard.sourceforge.net), variants were called by SAMtools (v0.1.19, 5). Gene structures were predicted by Cufflinks using RNA-Seq data derived from young leaf and panicle samples. The effect of each variant site was annotated by using snpEff (6).

Citation

Xu, X et al. (2011) Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nature Biotechnology 30:1-10.
Martin, M. (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17, 10-12.
Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760.
McKenna, A. et al. (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20:1297-303.
Li, H. et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079.
Cingolani, P. et al. (2012) A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly. 6(2):80-92.