- Reference_Nipponbare
- The Os-Nipponbare-Reference-IRGSP-1.0 (IRGSP1.0)
(http://rapdb.dna.affrc.go.jp/download/irgsp1.html)
At low magnifications (zoom out), the GC content plot of the reference sequence.
At high magnifications (zoom in), the actual DNA sequence.- Genes
- Gene set (the IRGSP1.0 genome sequence)
- Omachi Coverage(All)
- Omachi all read coverage
- Omachi Coverage(Unique)
- Omachi unique read coverage
- Omachi 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 annotation (Genes) downloaded from the GBrowse component of IRGSP 1.0. The gene region, which consisted of UTR5', CDS, and 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 CDS, UTR5' and UTR3' (UTRs), or other (introns) according to those positions. SNPs in the coding sequences were separated into synonymous and non-synonymous amino acid substitutions.- Omachi 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 annotation (Genes) downloaded from the GBrowse component of IRGSP 1.0. The gene region, which consisted of UTR5', CDS, and 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 CDS, UTR5' and UTR3' (UTRs), or other (introns) according to those positions. SNPs in the coding sequences were separated into synonymous and non-synonymous amino acid substitutions.- Omachi 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 annotation (Genes) downloaded from the GBrowse component of IRGSP 1.0. The gene region, which consisted of UTR5', CDS, and 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 CDS, UTR5' and UTR3' (UTRs), or other (introns) according to those positions. SNPs in the coding sequences were separated into synonymous and non-synonymous amino acid substitutions.- Yamadanishiki Coverage(All)
- Yamadanishiki all read coverage
- Yamadanishiki Coverage(Unique)
- Yamadanishiki unique read coverage
- Yamadanishiki SNP
- [Chr_position_Nipponbare_Yamadanishiki_call rate]
SNP positions were shown as blue triangles.
ex.) G -> A
Nipponbare sequence: G, Yamadanishiki sequence: A
Annotation Method
GFF files including positional information about the SNPs and InDels were constructed and annotated with a data set of RAP annotation (Genes) downloaded from the GBrowse component of IRGSP 1.0. The gene region, which consisted of UTR5', CDS, and 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 CDS, UTR5' and UTR3' (UTRs), or other (introns) according to those positions. SNPs in the coding sequences were separated into synonymous and non-synonymous amino acid substitutions.- Yamadanishiki Insertion
- [Chr_position_Nipponbare_Yamadanishiki_call rate]
Insertion positions were shown as red triangles.
ex.) G -> +AT
Nipponbare sequence: G, Yamadanishiki sequence: GAT
Annotation Method
GFF files including positional information about the SNPs and InDels were constructed and annotated with a data set of RAP annotation (Genes) downloaded from the GBrowse component of IRGSP 1.0. The gene region, which consisted of UTR5', CDS, and 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 CDS, UTR5' and UTR3' (UTRs), or other (introns) according to those positions. SNPs in the coding sequences were separated into synonymous and non-synonymous amino acid substitutions.- Yamadanishiki Deletion
- [Chr_position_Nipponbare_Yamadanishiki_call rate]
Deletion positions were shown as green triangles.
ex.) G -> -CC
Nipponbare sequence: GCC, Yamadanishiki sequence: G
Annotation Method
GFF files including positional information about the SNPs and InDels were constructed and annotated with a data set of RAP annotation (Genes) downloaded from the GBrowse component of IRGSP 1.0. The gene region, which consisted of UTR5', CDS, and 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 CDS, UTR5' and UTR3' (UTRs), or other (introns) according to those positions. SNPs in the coding sequences were separated into synonymous and non-synonymous amino acid substitutions.- Gohyakumangoku Coverage(All)
- Gohyakumangoku all read coverage
- Gohyakumangoku Coverage(Unique)
- Gohyakumangoku unique read coverage
- Gohyakumangoku SNP
- [Chr_position_Nipponbare_Gohyakumangoku_call rate]
SNP positions were shown as blue triangles.
ex.) G -> A
Nipponbare sequence: G, Gohyakumangoku sequence: A
Annotation Method
GFF files including positional information about the SNPs and InDels were constructed and annotated with a data set of RAP annotation (Genes) downloaded from the GBrowse component of IRGSP 1.0. The gene region, which consisted of UTR5', CDS, and 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 CDS, UTR5' and UTR3' (UTRs), or other (introns) according to those positions. SNPs in the coding sequences were separated into synonymous and non-synonymous amino acid substitutions.- Gohyakumangoku Insertion
- [Chr_position_Nipponbare_Gohyakumangoku_call rate]
Insertion positions were shown as red triangles.
ex.) G -> +AT
Nipponbare sequence: G, Gohyakumangoku sequence: GAT
Annotation Method
GFF files including positional information about the SNPs and InDels were constructed and annotated with a data set of RAP annotation (Genes) downloaded from the GBrowse component of IRGSP 1.0. The gene region, which consisted of UTR5', CDS, and 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 CDS, UTR5' and UTR3' (UTRs), or other (introns) according to those positions. SNPs in the coding sequences were separated into synonymous and non-synonymous amino acid substitutions.- Gohyakumangoku Deletion
- [Chr_position_Nipponbare_Gohyakumangoku_call rate]
Deletion positions were shown as green triangles.
ex.) G -> -CC
Nipponbare sequence: GCC, Gohyakumangoku sequence: G
Annotation Method
GFF files including positional information about the SNPs and InDels were constructed and annotated with a data set of RAP annotation (Genes) downloaded from the GBrowse component of IRGSP 1.0. The gene region, which consisted of UTR5', CDS, and 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 CDS, UTR5' and UTR3' (UTRs), or other (introns) according to those positions. SNPs in the coding sequences were separated into synonymous and non-synonymous amino acid substitutions.- Kameji Coverage(All)
- Kameji all read coverage
- Kameji Coverage(Unique)
- Kameji unique read coverage
- Kameji SNP
- [Chr_position_Nipponbare_Kameji_call rate]
SNP positions were shown as blue triangles.
ex.) G -> A
Nipponbare sequence: G, Kameji sequence: A
Annotation Method
GFF files including positional information about the SNPs and InDels were constructed and annotated with a data set of RAP annotation (Genes) downloaded from the GBrowse component of IRGSP 1.0. The gene region, which consisted of UTR5', CDS, and 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 CDS, UTR5' and UTR3' (UTRs), or other (introns) according to those positions. SNPs in the coding sequences were separated into synonymous and non-synonymous amino acid substitutions.- Kameji Insertion
- [Chr_position_Nipponbare_Kameji_call rate]
Insertion positions were shown as red triangles.
ex.) G -> +AT
Nipponbare sequence: G, Kameji sequence: GAT
Annotation Method
GFF files including positional information about the SNPs and InDels were constructed and annotated with a data set of RAP annotation (Genes) downloaded from the GBrowse component of IRGSP 1.0. The gene region, which consisted of UTR5', CDS, and 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 CDS, UTR5' and UTR3' (UTRs), or other (introns) according to those positions. SNPs in the coding sequences were separated into synonymous and non-synonymous amino acid substitutions.- Kameji Deletion
- [Chr_position_Nipponbare_Kameji_call rate]
Deletion positions were shown as green triangles.
ex.) G -> -CC
Nipponbare sequence: GCC, Kameji sequence: G
Annotation Method
GFF files including positional information about the SNPs and InDels were constructed and annotated with a data set of RAP annotation (Genes) downloaded from the GBrowse component of IRGSP 1.0. The gene region, which consisted of UTR5', CDS, and 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 CDS, UTR5' and UTR3' (UTRs), or other (introns) according to those positions. SNPs in the coding sequences were separated into synonymous and non-synonymous amino acid substitutions.- Koshihikari Coverage(All)
- Koshihikari all read coverage
- Koshihikari Coverage(Unique)
- Koshihikari unique read coverage
- Koshihikari SNP
- [Chr_position_Nipponbare_Koshihikari_call rate]
SNP positions were shown as blue triangles.
ex.) G -> A
Nipponbare sequence: G, Koshihikari sequence: A
Annotation Method
GFF files including positional information about the SNPs and InDels were constructed and annotated with a data set of RAP annotation (Genes) downloaded from the GBrowse component of IRGSP 1.0. The gene region, which consisted of UTR5', CDS, and 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 CDS, UTR5' and UTR3' (UTRs), or other (introns) according to those positions. SNPs in the coding sequences were separated into synonymous and non-synonymous amino acid substitutions.- Koshihikari Insertion
- [Chr_position_Nipponbare_Koshihikari_call rate]
Insertion positions were shown as red triangles.
ex.) G -> +AT
Nipponbare sequence: G, Koshihikari sequence: GAT
Annotation Method
GFF files including positional information about the SNPs and InDels were constructed and annotated with a data set of RAP annotation (Genes) downloaded from the GBrowse component of IRGSP 1.0. The gene region, which consisted of UTR5', CDS, and 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 CDS, UTR5' and UTR3' (UTRs), or other (introns) according to those positions. SNPs in the coding sequences were separated into synonymous and non-synonymous amino acid substitutions.- Koshihikari Deletion
- [Chr_position_Nipponbare_Koshihikari_call rate]
Deletion positions were shown as green triangles.
ex.) G -> -CC
Nipponbare sequence: GCC, Koshihikari sequence: G
Annotation Method
GFF files including positional information about the SNPs and InDels were constructed and annotated with a data set of RAP annotation (Genes) downloaded from the GBrowse component of IRGSP 1.0. The gene region, which consisted of UTR5', CDS, and 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 CDS, UTR5' and UTR3' (UTRs), or other (introns) according to those positions. SNPs in the coding sequences were separated into synonymous and non-synonymous amino acid substitutions.- Norin8 Coverage(All)
- Norin8 all read coverage
- Norin8 Coverage(Unique)
- Norin8 unique read coverage
- Norin8 SNP
- [Chr_position_Nipponbare_Norin8_call rate]
SNP positions were shown as blue triangles.
ex.) G -> A
Nipponbare sequence: G, Norin8 sequence: A
Annotation Method
GFF files including positional information about the SNPs and InDels were constructed and annotated with a data set of RAP annotation (Genes) downloaded from the GBrowse component of IRGSP 1.0. The gene region, which consisted of UTR5', CDS, and 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 CDS, UTR5' and UTR3' (UTRs), or other (introns) according to those positions. SNPs in the coding sequences were separated into synonymous and non-synonymous amino acid substitutions.- Norin8 Insertion
- [Chr_position_Nipponbare_Norin8_call rate]
Insertion positions were shown as red triangles.
ex.) G -> +AT
Nipponbare sequence: G, Norin8 sequence: GAT
Annotation Method
GFF files including positional information about the SNPs and InDels were constructed and annotated with a data set of RAP annotation (Genes) downloaded from the GBrowse component of IRGSP 1.0. The gene region, which consisted of UTR5', CDS, and 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 CDS, UTR5' and UTR3' (UTRs), or other (introns) according to those positions. SNPs in the coding sequences were separated into synonymous and non-synonymous amino acid substitutions.- Norin8 Deletion
- [Chr_position_Nipponbare_Norin8_call rate]
Deletion positions were shown as green triangles.
ex.) G -> -CC
Nipponbare sequence: GCC, Norin8 sequence: G
Annotation Method
GFF files including positional information about the SNPs and InDels were constructed and annotated with a data set of RAP annotation (Genes) downloaded from the GBrowse component of IRGSP 1.0. The gene region, which consisted of UTR5', CDS, and 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 CDS, UTR5' and UTR3' (UTRs), or other (introns) according to those positions. SNPs in the coding sequences were separated into synonymous and non-synonymous amino acid substitutions.- Moroberekan Coverage(All)
- Moroberekan all read coverage
- Moroberekan Coverage(Unique)
- Moroberekan unique read coverage
- Moroberekan SNP
- [Chr_position_Nipponbare_Moroberekan_call rate]
SNP positions were shown as blue triangles.
ex.) G -> A
Nipponbare sequence: G, Moroberekan sequence: A
Annotation Method
GFF files including positional information about the SNPs and InDels were constructed and annotated with a data set of RAP annotation (Genes) downloaded from the GBrowse component of IRGSP 1.0. The gene region, which consisted of UTR5', CDS, and 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 CDS, UTR5' and UTR3' (UTRs), or other (introns) according to those positions. SNPs in the coding sequences were separated into synonymous and non-synonymous amino acid substitutions.- Moroberekan Insertion
- [Chr_position_Nipponbare_Moroberekan_call rate]
Insertion positions were shown as red triangles.
ex.) G -> +AT
Nipponbare sequence: G, Moroberekan sequence: GAT
Annotation Method
GFF files including positional information about the SNPs and InDels were constructed and annotated with a data set of RAP annotation (Genes) downloaded from the GBrowse component of IRGSP 1.0. The gene region, which consisted of UTR5', CDS, and 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 CDS, UTR5' and UTR3' (UTRs), or other (introns) according to those positions. SNPs in the coding sequences were separated into synonymous and non-synonymous amino acid substitutions.- Moroberekan Deletion
- [Chr_position_Nipponbare_Moroberekan_call rate]
Deletion positions were shown as green triangles.
ex.) G -> -CC
Nipponbare sequence: GCC, Moroberekan sequence: G
Annotation Method
GFF files including positional information about the SNPs and InDels were constructed and annotated with a data set of RAP annotation (Genes) downloaded from the GBrowse component of IRGSP 1.0. The gene region, which consisted of UTR5', CDS, and 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 CDS, UTR5' and UTR3' (UTRs), or other (introns) according to those positions. SNPs in the coding sequences were separated into synonymous and non-synonymous amino acid substitutions.
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