- Coverage(Unique)
- unique read coverage
- Coverage(All)
- all read coverage
- Reference_Nipponbare
- Oryza sativa L.cv.Nipponbare, Pseudomolecules Build 4.0
(http://rgp.dna.affrc.go.jp/E/IRGSP/Build4/build4.htm)
At low magnifications (zoom out), the GC content plot of the reference sequence.
At high magnifications (zoom in), the actual DNA sequence.- SNP
- [Chr_position_Nipponbare_Omachi_call rate]
SNP positions were shown as blue triangles.
ex.) G -> A
Nipponbare sequence: G, Omachi sequence: A
Annotation Method
GFF files including positional information about the SNPs and InDels were constructed and annotated with a data set of RAP-DB2 transcripts (representative cDNA) downloaded from the GBrowse component of RAP-DB2. The gene region, which consisted of rep-UTR5', rep-CDS, and rep-UTR3', was listed in the data set along with data including positions, directions, and descriptions, which we used for annotations. SNPs and InDels in the gene region and other genome regions were annotated as genic and intergenic, respectively. The genic SNPs and InDels were classified as rep-CDS (coding sequences), rep-UTR5' and rep-UTR3' (UTRs), or other (introns) according to those positions. SNPs in the coding sequences were separated into synonymous and non-synonymous amino acid substitutions.- Insertion
- [Chr_position_Nipponbare_Omachi_call rate]
Insertion positions were shown as red triangles.
ex.) G -> +AT
Nipponbare sequence: G, Omachi sequence: GAT
Annotation Method
GFF files including positional information about the SNPs and InDels were constructed and annotated with a data set of RAP-DB2 transcripts (representative cDNA) downloaded from the GBrowse component of RAP-DB2. The gene region, which consisted of rep-UTR5', rep-CDS, and rep-UTR3', was listed in the data set along with data including positions, directions, and descriptions, which we used for annotations. SNPs and InDels in the gene region and other genome regions were annotated as genic and intergenic, respectively. The genic SNPs and InDels were classified as rep-CDS (coding sequences), rep-UTR5' and rep-UTR3' (UTRs), or other (introns) according to those positions. SNPs in the coding sequences were separated into synonymous and non-synonymous amino acid substitutions.- Deletion
- [Chr_position_Nipponbare_Omachi_call rate]
Deletion positions were shown as green triangles.
ex.) G -> -CC
Nipponbare sequence: GCC, Omachi sequence: G
Annotation Method
GFF files including positional information about the SNPs and InDels were constructed and annotated with a data set of RAP-DB2 transcripts (representative cDNA) downloaded from the GBrowse component of RAP-DB2. The gene region, which consisted of rep-UTR5', rep-CDS, and rep-UTR3', was listed in the data set along with data including positions, directions, and descriptions, which we used for annotations. SNPs and InDels in the gene region and other genome regions were annotated as genic and intergenic, respectively. The genic SNPs and InDels were classified as rep-CDS (coding sequences), rep-UTR5' and rep-UTR3' (UTRs), or other (introns) according to those positions. SNPs in the coding sequences were separated into synonymous and non-synonymous amino acid substitutions.- RAP2_locus
- The Rice Annotation Project Database release 2 (http://rapdb.dna.affrc.go.jp/ /archive/build4.html)
The Rice Annotation Project Database (RAP-DB): 2008 update (2008) Rice Annotation Project, Nucleic Acids Res., 36 (Database issue), D1028-33.
Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. (2007) Itoh, T., Tanaka, T. et al., Genome Res., 17, 175-83.- RAP2_transcript(representative_cDNA)
- Representative transcripts determined by rice FLcDNA.
- RAP2_transcript(representative_cDNA):frame_usage
- Each color corresponds to the 6-frame usage.
- RAP2_transcript(other_cDNAs)
- Non-representative transcripts determined by rice FLcDNA
- RAP2_transcript(other_cDNAs):frame_usage
- Each color corresponds to the 6-frame usage.
NGRC_Rice_Omachi
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