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Mutant Information

Mutant Name	FN400-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN400-S Alignment File
Seed Availability	Yes [Order Seeds]
Phenotype	TO:0000430 (Germination Rate) = Very Low (Below 24%) For more information, please see this phenotype file
Mapping (Hover to Zoom-In)

Variant Information

Single base substitutions: 27

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	28462357	C-T	HOMO	INTERGENIC
SBS	Chr3	6068579	A-G	HET	NON_SYNONYMOUS_CODING	LOC_Os03g11630
SBS	Chr3	10262719	A-C	HET	INTRON
SBS	Chr3	15130503	C-A	HET	INTERGENIC
SBS	Chr3	15130504	C-T	HET	INTERGENIC
SBS	Chr3	23255080	A-T	HET	INTERGENIC
SBS	Chr4	8129166	G-A	HET	INTERGENIC
SBS	Chr4	13343978	T-A	HET	INTERGENIC
SBS	Chr4	15234418	G-A	HET	INTERGENIC
SBS	Chr4	30686975	C-T	HET	SYNONYMOUS_CODING
SBS	Chr5	5353832	T-A	HET	INTERGENIC
SBS	Chr5	14846688	C-T	HET	INTERGENIC
SBS	Chr5	27931406	G-A	HET	INTERGENIC
SBS	Chr5	28946281	C-T	HET	INTRON
SBS	Chr6	13582910	A-G	HET	INTRON
SBS	Chr7	10055292	G-T	HET	INTERGENIC
SBS	Chr7	17498329	A-G	HET	INTERGENIC
SBS	Chr7	28504945	G-C	HET	SYNONYMOUS_CODING
SBS	Chr9	16210852	T-A	HOMO	NON_SYNONYMOUS_CODING	LOC_Os09g26680
SBS	Chr10	17431236	C-T	HET	INTERGENIC
SBS	Chr10	17932932	T-A	HET	INTERGENIC
SBS	Chr10	21511777	C-T	HET	SYNONYMOUS_CODING
SBS	Chr10	21511778	A-T	HET	STOP_GAINED	LOC_Os10g40180
SBS	Chr11	13781623	C-T	HET	INTRON
SBS	Chr11	15316994	T-C	HET	INTRON
SBS	Chr11	21587799	A-T	HET	INTERGENIC
SBS	Chr11	28805099	G-C	HET	INTRON

Deletions: 21

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Deletion	Chr5	1516634	1516640	6
Deletion	Chr7	2563211	2563217	6
Deletion	Chr5	3291361	3291366	5
Deletion	Chr2	5305990	5306055	65	LOC_Os02g10130
Deletion	Chr9	8518123	8518128	5
Deletion	Chr4	8627349	8627352	3
Deletion	Chr6	11642657	11642682	25
Deletion	Chr4	13343973	13343974	1
Deletion	Chr2	14376407	14376450	43	LOC_Os02g24780
Deletion	Chr4	19209831	19209832	1
Deletion	Chr2	19344170	19344174	4
Deletion	Chr4	19662121	19662124	3
Deletion	Chr11	21717837	21717844	7
Deletion	Chr2	21810901	21810904	3	LOC_Os02g36190
Deletion	Chr2	22020193	22020202	9
Deletion	Chr3	24081621	24081625	4
Deletion	Chr11	25636001	25970000	334000	47
Deletion	Chr8	25901864	25901935	71
Deletion	Chr11	25972001	26613000	641000	96
Deletion	Chr5	28939400	28939433	33
Deletion	Chr4	29492001	29538000	46000	9

Insertions: 2

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Insertion	Chr5	23220230	23220233	4
Insertion	Chr7	12851170	12851171	2

Inversions: 2

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr8	1411551	1919231
Inversion	Chr9	10240858	10395821

No Translocation

Tandem duplications: 1

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Tandem Duplication	Chr9	10240875	12762073	2521198	373

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