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Mutant Information

Mutant Name	FN1142-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN1142-S Alignment File
Seed Availability	Yes [Order Seeds]
Phenotype	TO:0000430 (Germination Rate) = Low (Between 25% and 75%) For more information, please see this phenotype file
Mapping (Hover to Zoom-In)

Variant Information

Single base substitutions: 30

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr10	12134604	C-T	HOMO	INTRON
SBS	Chr10	20548092	T-C	HOMO	INTERGENIC
SBS	Chr10	4634833	C-T	HET	INTRON
SBS	Chr10	9009080	C-T	HOMO	INTRON
SBS	Chr10	9537065	T-A	HOMO	INTERGENIC
SBS	Chr11	25345105	C-G	HOMO	NON_SYNONYMOUS_CODING	LOC_Os11g42090
SBS	Chr11	25345117	A-G	HOMO	NON_SYNONYMOUS_CODING	LOC_Os11g42090
SBS	Chr11	4422481	C-T	HET	SYNONYMOUS_CODING
SBS	Chr12	15791335	G-T	HET	INTERGENIC
SBS	Chr12	21838761	A-G	HOMO	NON_SYNONYMOUS_CODING	LOC_Os12g35840
SBS	Chr12	22394803	A-G	HOMO	SYNONYMOUS_CODING
SBS	Chr2	22266472	C-A	HET	INTERGENIC
SBS	Chr2	28416326	G-T	HET	INTERGENIC
SBS	Chr2	35138880	T-C	HOMO	INTERGENIC
SBS	Chr2	9060305	A-T	HET	INTERGENIC
SBS	Chr3	17355056	A-T	HET	INTERGENIC
SBS	Chr3	20833183	G-A	HET	INTRON
SBS	Chr4	24600062	T-C	HET	INTRON
SBS	Chr4	34499168	C-T	HOMO	SYNONYMOUS_CODING
SBS	Chr5	14608530	A-G	HOMO	INTERGENIC
SBS	Chr5	17222661	A-G	HET	INTERGENIC
SBS	Chr5	5704301	A-G	HET	INTERGENIC
SBS	Chr6	28878719	C-A	HET	INTERGENIC
SBS	Chr7	14221291	C-T	HET	INTERGENIC
SBS	Chr7	23462469	G-A	HET	INTERGENIC
SBS	Chr7	8770592	A-T	HET	INTERGENIC
SBS	Chr8	20459007	C-A	HET	INTERGENIC
SBS	Chr8	7473581	G-A	HOMO	INTERGENIC
SBS	Chr9	17002527	G-A	HET	INTERGENIC
SBS	Chr9	22269035	G-T	HET	INTERGENIC

Deletions: 22

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Deletion	Chr3	890634	890641	7
Deletion	Chr1	4675278	4675293	15	LOC_Os01g09246
Deletion	Chr1	4698235	4698241	6	LOC_Os01g09260
Deletion	Chr1	5145131	5145143	12
Deletion	Chr1	5145525	5145527	2
Deletion	Chr3	6551482	6551509	27
Deletion	Chr4	10038443	10038451	8
Deletion	Chr2	10099083	10099114	31
Deletion	Chr7	11020752	11020753	1
Deletion	Chr5	11242512	11242532	20
Deletion	Chr9	15562556	15562557	1
Deletion	Chr7	20011300	20019054	7754	LOC_Os07g33480
Deletion	Chr4	20114761	20114766	5
Deletion	Chr12	21437318	21437343	25	LOC_Os12g35280
Deletion	Chr12	21826469	21826476	7	LOC_Os12g35810
Deletion	Chr3	22684001	22862000	178000	27
Deletion	Chr12	22789980	22789981	1
Deletion	Chr5	24165586	24165602	16
Deletion	Chr8	24714201	24714202	1	LOC_Os08g39120
Deletion	Chr11	24796680	24796695	15
Deletion	Chr11	25320530	25320531	1
Deletion	Chr8	28046739	28046746	7

Insertions: 3

Variant Type	Chromosome	Start	End	Size (bp)
Insertion	Chr2	18552323	18552324	2
Insertion	Chr4	27397034	27397035	2
Insertion	Chr8	2994270	2994271	2

No Inversion

Translocations: 2

Variant Type	Chromosome	Position 1	Chromosome	Position 2	Number of Genes
Translocation	Chr7	23875811	Chr2	34843856	LOC_Os02g56850
Translocation	Chr7	23877006	Chr2	34843846	LOC_Os02g56850

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