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Mutant Information

Mutant Name	FN1278-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN1278-S Alignment File
Seed Availability	Yes [Order Seeds]
Phenotype	TO:0000014 (Panicle Weight) = Low (Between 25% and 74%) TO:0000207 (Plant height) = Normal (Between 75% and 125%) TO:0000445 (Seed Number) = Low (Between 25% and 74%) TO:0000639 (Seed fertility) = Normal (Between 75% and 125%) For more information, please see this phenotype file
Mapping (Hover to Zoom-In)

Variant Information

Single base substitutions: 50

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	11608707	C-A	HET	INTERGENIC
SBS	Chr1	13236707	A-T	HET	INTERGENIC
SBS	Chr1	18502084	G-A	HOMO	INTERGENIC
SBS	Chr1	19626536	G-A	HOMO	NON_SYNONYMOUS_CODING	LOC_Os01g35470
SBS	Chr1	2958775	T-A	HOMO	INTERGENIC
SBS	Chr1	34209005	T-A	HET	INTRON
SBS	Chr1	34209006	T-A	HET	INTRON
SBS	Chr1	41043808	G-A	HET	INTERGENIC
SBS	Chr1	5431653	A-T	HOMO	INTERGENIC
SBS	Chr1	5995170	C-T	HOMO	SYNONYMOUS_CODING
SBS	Chr10	23053497	A-T	HET	SPLICE_SITE_REGION
SBS	Chr10	23053498	C-A	HET	SPLICE_SITE_REGION
SBS	Chr10	9048183	G-A	HET	NON_SYNONYMOUS_CODING	LOC_Os10g17900
SBS	Chr11	6250398	A-C	HET	NON_SYNONYMOUS_CODING	LOC_Os11g11290
SBS	Chr11	9316026	G-A	HET	NON_SYNONYMOUS_CODING	LOC_Os11g16790
SBS	Chr11	9728930	G-A	HET	INTERGENIC
SBS	Chr11	9728932	G-A	HET	INTERGENIC
SBS	Chr11	9728935	T-A	HET	INTERGENIC
SBS	Chr12	11207680	T-C	HET	INTERGENIC
SBS	Chr12	17846224	G-T	HET	INTERGENIC
SBS	Chr12	23011274	T-C	HOMO	INTRON
SBS	Chr12	26875728	T-C	HOMO	INTRON
SBS	Chr12	8168331	G-T	HET	INTERGENIC
SBS	Chr12	9030948	A-C	HET	INTRON
SBS	Chr2	17213996	A-G	HOMO	INTRON
SBS	Chr2	17214370	A-G	HOMO	INTRON
SBS	Chr2	23561874	G-A	HET	INTERGENIC
SBS	Chr2	30190365	C-G	HET	SPLICE_SITE_REGION
SBS	Chr2	6575279	A-T	HOMO	INTRON
SBS	Chr3	16792857	C-A	HET	INTERGENIC
SBS	Chr3	21145250	C-G	HET	INTERGENIC
SBS	Chr3	25078048	T-C	HET	INTERGENIC
SBS	Chr3	4839864	T-C	HET	INTERGENIC
SBS	Chr4	12999371	G-T	HOMO	SYNONYMOUS_CODING
SBS	Chr4	14875767	T-A	HOMO	INTERGENIC
SBS	Chr4	26293214	C-T	HOMO	INTERGENIC
SBS	Chr5	10714491	T-C	HOMO	INTERGENIC
SBS	Chr5	1141702	C-T	HET	INTERGENIC
SBS	Chr5	13594042	T-C	HOMO	INTRON
SBS	Chr5	5108442	A-G	HOMO	INTERGENIC
SBS	Chr6	12988236	G-T	HET	NON_SYNONYMOUS_CODING	LOC_Os06g22370
SBS	Chr6	13176802	C-A	HET	INTERGENIC
SBS	Chr6	13827410	G-A	HOMO	INTERGENIC
SBS	Chr6	17185842	C-G	HET	INTERGENIC
SBS	Chr6	27669943	A-G	HOMO	SYNONYMOUS_CODING
SBS	Chr7	16695555	G-A	HET	SYNONYMOUS_CODING
SBS	Chr8	15340786	C-T	HOMO	INTERGENIC
SBS	Chr9	4886230	A-G	HOMO	INTRON
SBS	Chr9	5257029	T-C	HOMO	SYNONYMOUS_CODING
SBS	Chr9	8218304	C-G	HOMO	INTERGENIC

Deletions: 33

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Deletion	Chr10	219125	219128	3
Deletion	Chr9	297889	297899	10
Deletion	Chr6	621173	621178	5
Deletion	Chr7	6502471	6502476	5
Deletion	Chr8	6788458	6788481	23
Deletion	Chr3	7454642	7454643	1
Deletion	Chr7	7522401	7522406	5
Deletion	Chr4	8174288	8174299	11
Deletion	Chr10	10132966	10132977	11	LOC_Os10g20180
Deletion	Chr9	10162636	10162637	1
Deletion	Chr8	10954773	10954776	3
Deletion	Chr7	11687148	11687151	3	LOC_Os07g20270
Deletion	Chr11	11699922	11699923	1
Deletion	Chr11	11803747	11803764	17
Deletion	Chr12	12758354	12758368	14
Deletion	Chr1	14062934	14236935	174001	25
Deletion	Chr8	17551901	17551941	40
Deletion	Chr2	17911281	17911290	9	LOC_Os02g30150
Deletion	Chr4	19128716	19128724	8
Deletion	Chr8	21270224	21270226	2
Deletion	Chr8	21947344	21947350	6
Deletion	Chr3	23523199	23523206	7
Deletion	Chr6	24088460	24088464	4
Deletion	Chr3	24160296	24160297	1
Deletion	Chr1	24358226	24358227	1
Deletion	Chr6	24521563	24521573	10
Deletion	Chr7	27249307	27249312	5
Deletion	Chr2	31168691	31168694	3
Deletion	Chr2	32453196	32453204	8
Deletion	Chr2	32901213	32901221	8
Deletion	Chr3	34941315	34941325	10	LOC_Os03g61630
Deletion	Chr2	35327026	35330134	3108	LOC_Os02g57690
Deletion	Chr1	38914084	38914093	9

Insertions: 5

Variant Type	Chromosome	Start	End	Size (bp)
Insertion	Chr1	11768578	11768579	2
Insertion	Chr10	1960647	1960647	1
Insertion	Chr11	25763332	25763335	4
Insertion	Chr7	19471453	19471453	1
Insertion	Chr7	19981738	19981738	1

No Inversion

Translocations: 6

Variant Type	Chromosome	Position 1	Chromosome	Position 2	Number of Genes
Translocation	Chr8	2324484	Chr2	10167366
Translocation	Chr6	14778297	Chr3	5107995
Translocation	Chr6	14779253	Chr3	5107974
Translocation	Chr11	22349561	Chr3	5107950
Translocation	Chr3	29049448	Chr2	35330132	LOC_Os02g57690
Translocation	Chr3	29049459	Chr2	35327035	LOC_Os02g57690

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