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Mutant Information

Mutant Name	FN828-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN828-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	Chr1	12983034	C-A	HET	INTERGENIC
SBS	Chr1	17996391	C-T	HOMO	SYNONYMOUS_CODING
SBS	Chr1	28962461	C-T	HET	INTERGENIC
SBS	Chr1	317625	G-C	HOMO	INTERGENIC
SBS	Chr10	13481603	A-T	HOMO	INTERGENIC
SBS	Chr10	1945080	G-A	HET	SYNONYMOUS_CODING
SBS	Chr10	8377240	C-G	HET	INTRON
SBS	Chr11	12876313	C-T	HOMO	SYNONYMOUS_CODING
SBS	Chr11	21994690	T-C	HOMO	INTERGENIC
SBS	Chr11	3926507	A-T	HET	NON_SYNONYMOUS_CODING	LOC_Os11g07690
SBS	Chr2	19476327	C-T	HET	INTRON
SBS	Chr2	22967334	T-C	HET	INTERGENIC
SBS	Chr2	34763202	G-C	HET	INTERGENIC
SBS	Chr3	11021226	C-T	HET	NON_SYNONYMOUS_CODING	LOC_Os03g19590
SBS	Chr3	15897234	C-T	HET	INTERGENIC
SBS	Chr3	26262907	C-A	HET	INTRON
SBS	Chr3	28984926	A-G	HOMO	INTERGENIC
SBS	Chr3	4986403	T-C	HET	INTRON
SBS	Chr4	14547660	G-A	HOMO	INTERGENIC
SBS	Chr4	14769625	C-T	HOMO	NON_SYNONYMOUS_CODING	LOC_Os04g25470
SBS	Chr4	4944539	G-A	HOMO	NON_SYNONYMOUS_CODING	LOC_Os04g09310
SBS	Chr5	3579783	C-T	HOMO	INTERGENIC
SBS	Chr5	4229808	A-G	HET	INTERGENIC
SBS	Chr6	12648210	G-A	HET	INTERGENIC
SBS	Chr6	17031500	C-T	HET	INTERGENIC
SBS	Chr6	1722310	G-A	HOMO	INTERGENIC
SBS	Chr6	1722311	C-A	HOMO	INTERGENIC
SBS	Chr6	8526061	G-C	HOMO	INTERGENIC
SBS	Chr7	19846990	C-T	HOMO	INTERGENIC
SBS	Chr9	5853697	G-A	HET	INTERGENIC

Deletions: 17

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Deletion	Chr9	2948851	2948853	2
Deletion	Chr6	4077006	4077010	4
Deletion	Chr10	4757371	4757375	4
Deletion	Chr10	4933518	4933519	1
Deletion	Chr11	7064065	7064067	2
Deletion	Chr3	9580492	9580499	7
Deletion	Chr10	9973126	9973130	4
Deletion	Chr8	13364199	13364202	3
Deletion	Chr1	15562167	15562173	6
Deletion	Chr8	16212678	16212679	1
Deletion	Chr6	16809159	16809161	2
Deletion	Chr3	19340868	19340870	2	LOC_Os03g33860
Deletion	Chr2	20923855	20923862	7
Deletion	Chr5	24201865	24201866	1
Deletion	Chr5	24568478	24568481	3
Deletion	Chr6	25857717	25857723	6
Deletion	Chr2	30994195	30994196	1

Insertions: 4

Variant Type	Chromosome	Start	End	Size (bp)
Insertion	Chr11	23208034	23208036	3
Insertion	Chr11	28660277	28660278	2
Insertion	Chr12	18733654	18733655	2
Insertion	Chr12	20273415	20273416	2

Inversions: 1

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr3	24192281	24765568	LOC_Os03g43390

No Translocation

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