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Mutant Information

Mutant Name	FN1239-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN1239-S Alignment File
Seed Availability	Yes [Order Seeds]
Phenotype	TO:0000326 (Leaf Color) = Normal TO:0000137 (Days to heading) = Normal (Between 75% and 125%) TO:0000346 (Tiller number) = Normal (Between 75% and 125%) TO:0000430 (Germination Rate) = Normal (Between 75% and 125%) For more information, please see this phenotype file
Mapping (Hover to Zoom-In)

Variant Information

Single base substitutions: 31

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	36315782	G-A	HOMO	NON_SYNONYMOUS_CODING	LOC_Os01g62710
SBS	Chr3	1851946	T-C	HOMO	INTERGENIC
SBS	Chr3	14274509	G-C	HOMO	INTERGENIC
SBS	Chr3	31825294	A-C	HET	INTERGENIC
SBS	Chr4	2110223	C-T	HOMO	INTRON
SBS	Chr4	20797470	C-T	HOMO	INTERGENIC
SBS	Chr4	26077566	T-C	HOMO	INTERGENIC
SBS	Chr5	6519464	T-A	HOMO	INTERGENIC
SBS	Chr5	10562716	G-A	HOMO	NON_SYNONYMOUS_CODING	LOC_Os05g18340
SBS	Chr5	18633306	G-C	HOMO	INTERGENIC
SBS	Chr6	12318935	G-T	HOMO	NON_SYNONYMOUS_CODING	LOC_Os06g21330
SBS	Chr6	21704466	A-T	HET	INTERGENIC
SBS	Chr6	26970460	G-A	HET	INTERGENIC
SBS	Chr7	18984209	A-T	HOMO	INTERGENIC
SBS	Chr7	20532060	C-A	HET	INTERGENIC
SBS	Chr7	21891904	C-T	HET	INTERGENIC
SBS	Chr8	10898418	G-A	HET	INTERGENIC
SBS	Chr8	11149138	A-G	HET	INTRON
SBS	Chr9	8739108	G-A	HET	SPLICE_SITE_REGION
SBS	Chr9	12247475	C-A	HET	INTERGENIC
SBS	Chr9	19733070	C-T	HET	INTRON
SBS	Chr10	7531445	C-A	HET	INTERGENIC
SBS	Chr10	13340489	G-A	HET	INTERGENIC
SBS	Chr10	15736430	C-T	HET	INTRON
SBS	Chr11	16607638	G-A	HET	INTERGENIC
SBS	Chr11	18366980	G-A	HET	INTERGENIC
SBS	Chr11	25105567	T-C	HET	NON_SYNONYMOUS_CODING	LOC_Os11g41780
SBS	Chr12	1010240	A-T	HET	INTRON
SBS	Chr12	1308875	G-A	HET	INTERGENIC
SBS	Chr12	22106376	G-A	HOMO	INTERGENIC
SBS	Chr12	23557149	A-T	HOMO	INTRON

Deletions: 23

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Deletion	Chr11	821222	840537	19315	4
Deletion	Chr12	1010234	1010235	1
Deletion	Chr10	1022129	1022136	7
Deletion	Chr7	2853247	2853253	6
Deletion	Chr2	3680139	3680141	2
Deletion	Chr4	6832706	6832711	5
Deletion	Chr8	8432682	8432686	4
Deletion	Chr11	9186016	9186021	5
Deletion	Chr7	9410173	9410181	8
Deletion	Chr11	10085816	10085840	24
Deletion	Chr2	16336227	16336239	12
Deletion	Chr3	16797786	16797787	1
Deletion	Chr4	19853714	19854383	669	LOC_Os04g32880
Deletion	Chr1	19891137	19891144	7
Deletion	Chr11	20054806	20054811	5
Deletion	Chr5	24341956	24341977	21
Deletion	Chr3	26360719	26360723	4
Deletion	Chr8	26627413	26627415	2	LOC_Os08g42140
Deletion	Chr5	27028245	27028248	3
Deletion	Chr1	27787472	27787476	4
Deletion	Chr6	29419401	29419402	1
Deletion	Chr1	31974333	31974342	9
Deletion	Chr1	40573094	40573095	1	LOC_Os01g70110

Insertions: 1

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Insertion	Chr2	23677131	23677132	2

Inversions: 4

Variant Type	Chromosome	Position 1	Position 2
Inversion	Chr8	2117185	2551050
Inversion	Chr8	2298964	2551047
Inversion	Chr11	6437714	6886447
Inversion	Chr1	19367628	19374041

Translocations: 3

Variant Type	Chromosome	Position 1	Chromosome	Position 2	Number of Genes
Translocation	Chr12	1233914	Chr4	19853724	LOC_Os04g32880
Translocation	Chr5	1243253	Chr3	15012905	LOC_Os05g03120
Translocation	Chr5	9647478	Chr3	14097981	LOC_Os03g24730

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