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Mutant Information

SOS indicates the sequenced line is sterile and seeds from siblings are available.

Mutant Name	FN554-S [Download]
Generation	M2-SOS
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN554-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: 32

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	12990180	C-T	HET	SYNONYMOUS_CODING
SBS	Chr1	19258586	C-A	HET	STOP_GAINED	LOC_Os01g34880
SBS	Chr1	25641334	C-T	HET	INTRON
SBS	Chr1	30057242	A-T	HOMO	INTERGENIC
SBS	Chr1	39380628	C-T	HET	INTERGENIC
SBS	Chr11	13984158	T-C	HET	INTERGENIC
SBS	Chr11	900357	A-G	HET	INTERGENIC
SBS	Chr12	11281045	T-C	HOMO	INTERGENIC
SBS	Chr12	19395618	C-A	HET	INTERGENIC
SBS	Chr12	25512402	C-T	HET	NON_SYNONYMOUS_CODING	LOC_Os12g41170
SBS	Chr2	2213546	A-T	HET	INTRON
SBS	Chr3	15358664	A-G	HET	INTERGENIC
SBS	Chr3	15497178	C-T	HOMO	INTERGENIC
SBS	Chr3	20763029	C-T	HOMO	INTERGENIC
SBS	Chr3	29683698	A-T	HET	INTERGENIC
SBS	Chr4	12457870	T-C	HET	INTERGENIC
SBS	Chr4	1286121	T-A	HOMO	INTERGENIC
SBS	Chr4	18525660	A-G	HOMO	INTRON
SBS	Chr4	34226290	T-C	HET	INTERGENIC
SBS	Chr5	15685068	C-T	HOMO	INTRON
SBS	Chr5	8574267	C-T	HOMO	INTRON
SBS	Chr5	8574268	C-T	HOMO	INTRON
SBS	Chr6	7046354	C-T	HET	INTERGENIC
SBS	Chr7	14163576	C-T	HOMO	INTRON
SBS	Chr7	16673422	G-A	HOMO	INTERGENIC
SBS	Chr7	16857990	T-C	HOMO	INTRON
SBS	Chr8	20756214	A-G	HET	INTERGENIC
SBS	Chr8	5759021	A-G	HET	INTERGENIC
SBS	Chr8	8886004	A-T	HET	INTRON
SBS	Chr8	9665570	A-T	HET	INTERGENIC
SBS	Chr9	21210340	A-G	HET	INTRON
SBS	Chr9	3394591	T-C	HET	INTRON

Deletions: 14

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Deletion	Chr1	1532060	1532063	3
Deletion	Chr6	2712032	2712078	46	LOC_Os06g05920
Deletion	Chr6	6143762	6143765	3
Deletion	Chr11	6220635	6220636	1	LOC_Os11g11240
Deletion	Chr1	9110056	9110057	1
Deletion	Chr1	13019001	13081000	62000	10
Deletion	Chr7	13460958	13460965	7
Deletion	Chr1	16728646	16728647	1
Deletion	Chr7	17121826	17121833	7
Deletion	Chr2	18360853	18360856	3
Deletion	Chr7	18547306	18547317	11
Deletion	Chr12	19811551	19811555	4
Deletion	Chr5	23716351	23716353	2
Deletion	Chr4	27531220	27531232	12

Insertions: 6

Variant Type	Chromosome	Start	End	Size (bp)
Insertion	Chr1	2580941	2580944	4
Insertion	Chr2	30921509	30921516	8
Insertion	Chr2	31487063	31487064	2
Insertion	Chr8	16701441	16701442	2
Insertion	Chr9	14655697	14655697	1
Insertion	Chr9	9197671	9197672	2

No Inversion

Translocations: 1

Variant Type	Chromosome	Position 1	Chromosome	Position 2	Number of Genes
Translocation	Chr10	8892757	Chr7	24229880	2

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