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Mutant Information

Mutant Name	FN2628-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN2628-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

Variant Information

Single base substitutions: 40

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 14219448 A-C Hetero INTRON
SBS Chr1 29595551 G-A Hetero INTRON
SBS Chr1 40376889 A-C Homo INTERGENIC
SBS Chr1 42609881 T-C Hetero INTRON
SBS Chr2 4022064 C-T Hetero INTERGENIC
SBS Chr2 4905428 T-A Homo INTERGENIC
SBS Chr2 11785153 G-C Hetero INTERGENIC
SBS Chr2 17412357 T-A Hetero UTR_5_PRIME
SBS Chr2 25385880 A-T Hetero INTERGENIC
SBS Chr2 26684099 C-T Hetero INTERGENIC
SBS Chr3 6397724 T-G Homo INTERGENIC
SBS Chr3 18799520 A-T Hetero INTERGENIC
SBS Chr3 18799524 A-G Hetero INTERGENIC
SBS Chr3 20454869 C-T Hetero INTERGENIC
SBS Chr3 23390886 A-C Hetero INTERGENIC
SBS Chr3 25388061 C-T Hetero INTRON
SBS Chr3 30297301 C-G Hetero INTERGENIC
SBS Chr3 36289482 C-T Hetero INTERGENIC
SBS Chr4 7226871 G-T Hetero INTERGENIC
SBS Chr4 9978861 G-A Hetero INTERGENIC
SBS Chr4 18916559 G-A Hetero UTR_3_PRIME
SBS Chr5 9605715 C-A Hetero INTERGENIC
SBS Chr5 13504918 A-G Homo INTERGENIC
SBS Chr6 8198813 G-C Hetero INTERGENIC
SBS Chr6 15505936 G-A Hetero INTERGENIC
SBS Chr6 17636648 A-T Hetero INTERGENIC
SBS Chr6 17655083 C-T Hetero INTERGENIC
SBS Chr6 19125112 A-G Hetero INTERGENIC
SBS Chr7 1307805 A-G Hetero INTERGENIC
SBS Chr7 5570817 T-C Homo NON_SYNONYMOUS_CODING OsKitaake07g067700
SBS Chr7 7550962 A-G Homo INTERGENIC
SBS Chr7 8629322 A-G Homo INTERGENIC
SBS Chr8 17148683 C-T Hetero INTERGENIC
SBS Chr8 21932954 G-A Hetero INTERGENIC
SBS Chr8 28895433 C-T Homo NON_SYNONYMOUS_CODING OsKitaake08g249800
SBS Chr9 8339153 C-T Hetero INTERGENIC
SBS Chr9 14113019 T-A Hetero INTRON
SBS Chr9 19263921 G-T Hetero NON_SYNONYMOUS_CODING OsKitaake09g155700
SBS Chr11 22992348 T-C Hetero INTRON
SBS Chr12 23413119 T-A Hetero INTERGENIC

Deletions: 15

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr11 173001 348000 174999 26
Deletion Chr9 578001 623000 44999 OsKitaake09g004400
Deletion Chr11 1574104 1574108 4
Deletion Chr6 3980266 3980268 2
Deletion Chr12 7789304 7789306 2
Deletion Chr6 9165380 9165384 4
Deletion Chr1 10269037 10269040 3
Deletion Chr3 13706601 13706602 1
Deletion Chr4 19439001 19448000 8999 OsKitaake04g099601
Deletion Chr7 19975549 19975571 22
Deletion Chr3 22363954 22363962 8
Deletion Chr7 23802791 23802808 17
Deletion Chr7 29078445 29078449 4
Deletion Chr1 29110748 29110750 2 OsKitaake01g282900
Deletion Chr1 35930582 35930583 1

Insertions: 4

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr1 7996282 7996286 3
Insertion Chr1 44244958 44244961 2
Insertion Chr8 16551552 16551555 2
Insertion Chr11 29194355 29194360 4

Translocations: 4

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes

Translocation Chr9 578608 Chr1 8918537
Translocation Chr9 619290 Chr1 8918280
Translocation Chr12 6379586 Chr3 4803073 2
Translocation Chr9 20339020 Chr3 4803074 2

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	14219448	A-C	Hetero	INTRON
SBS	Chr1	29595551	G-A	Hetero	INTRON
SBS	Chr1	40376889	A-C	Homo	INTERGENIC
SBS	Chr1	42609881	T-C	Hetero	INTRON
SBS	Chr2	4022064	C-T	Hetero	INTERGENIC
SBS	Chr2	4905428	T-A	Homo	INTERGENIC
SBS	Chr2	11785153	G-C	Hetero	INTERGENIC
SBS	Chr2	17412357	T-A	Hetero	UTR_5_PRIME
SBS	Chr2	25385880	A-T	Hetero	INTERGENIC
SBS	Chr2	26684099	C-T	Hetero	INTERGENIC
SBS	Chr3	6397724	T-G	Homo	INTERGENIC
SBS	Chr3	18799520	A-T	Hetero	INTERGENIC
SBS	Chr3	18799524	A-G	Hetero	INTERGENIC
SBS	Chr3	20454869	C-T	Hetero	INTERGENIC
SBS	Chr3	23390886	A-C	Hetero	INTERGENIC
SBS	Chr3	25388061	C-T	Hetero	INTRON
SBS	Chr3	30297301	C-G	Hetero	INTERGENIC
SBS	Chr3	36289482	C-T	Hetero	INTERGENIC
SBS	Chr4	7226871	G-T	Hetero	INTERGENIC
SBS	Chr4	9978861	G-A	Hetero	INTERGENIC
SBS	Chr4	18916559	G-A	Hetero	UTR_3_PRIME
SBS	Chr5	9605715	C-A	Hetero	INTERGENIC
SBS	Chr5	13504918	A-G	Homo	INTERGENIC
SBS	Chr6	8198813	G-C	Hetero	INTERGENIC
SBS	Chr6	15505936	G-A	Hetero	INTERGENIC
SBS	Chr6	17636648	A-T	Hetero	INTERGENIC
SBS	Chr6	17655083	C-T	Hetero	INTERGENIC
SBS	Chr6	19125112	A-G	Hetero	INTERGENIC
SBS	Chr7	1307805	A-G	Hetero	INTERGENIC
SBS	Chr7	5570817	T-C	Homo	NON_SYNONYMOUS_CODING	OsKitaake07g067700
SBS	Chr7	7550962	A-G	Homo	INTERGENIC
SBS	Chr7	8629322	A-G	Homo	INTERGENIC
SBS	Chr8	17148683	C-T	Hetero	INTERGENIC
SBS	Chr8	21932954	G-A	Hetero	INTERGENIC
SBS	Chr8	28895433	C-T	Homo	NON_SYNONYMOUS_CODING	OsKitaake08g249800
SBS	Chr9	8339153	C-T	Hetero	INTERGENIC
SBS	Chr9	14113019	T-A	Hetero	INTRON
SBS	Chr9	19263921	G-T	Hetero	NON_SYNONYMOUS_CODING	OsKitaake09g155700
SBS	Chr11	22992348	T-C	Hetero	INTRON
SBS	Chr12	23413119	T-A	Hetero	INTERGENIC

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr11	173001	348000	174999	26
Deletion	Chr9	578001	623000	44999	OsKitaake09g004400
Deletion	Chr11	1574104	1574108	4
Deletion	Chr6	3980266	3980268	2
Deletion	Chr12	7789304	7789306	2
Deletion	Chr6	9165380	9165384	4
Deletion	Chr1	10269037	10269040	3
Deletion	Chr3	13706601	13706602	1
Deletion	Chr4	19439001	19448000	8999	OsKitaake04g099601
Deletion	Chr7	19975549	19975571	22
Deletion	Chr3	22363954	22363962	8
Deletion	Chr7	23802791	23802808	17
Deletion	Chr7	29078445	29078449	4
Deletion	Chr1	29110748	29110750	2	OsKitaake01g282900
Deletion	Chr1	35930582	35930583	1

Variant Type	Chromosome	Position 1	Chromosome	Position 2	Number of Genes
Translocation	Chr9	578608	Chr1	8918537
Translocation	Chr9	619290	Chr1	8918280
Translocation	Chr12	6379586	Chr3	4803073	2
Translocation	Chr9	20339020	Chr3	4803074	2

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Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes