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Mutant Information

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

Mutant Name	FN1315-S [Download]
Generation	M2-SOS
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN1315-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: 35

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 21616904 C-A Homo INTERGENIC
SBS Chr1 28258026 C-A Hetero INTERGENIC
SBS Chr2 13312260 C-T Hetero INTRON
SBS Chr2 15564579 G-T Hetero INTERGENIC
SBS Chr2 17764863 G-C Hetero UTR_5_PRIME
SBS Chr3 16178337 C-A Hetero INTERGENIC
SBS Chr3 22918122 T-A Hetero INTERGENIC
SBS Chr3 23511412 C-A Hetero INTERGENIC
SBS Chr3 34425196 C-T Homo INTERGENIC
SBS Chr4 6081658 C-T Hetero INTERGENIC
SBS Chr4 20612191 G-A Homo SYNONYMOUS_CODING
SBS Chr4 21133405 C-T Homo INTRON
SBS Chr4 24902003 T-G Hetero INTERGENIC
SBS Chr4 27276516 C-T Hetero INTERGENIC
SBS Chr4 28087754 A-G Hetero INTERGENIC
SBS Chr5 7050707 T-C Hetero INTERGENIC
SBS Chr5 22810573 C-T Homo INTERGENIC
SBS Chr5 27817612 G-A Homo SYNONYMOUS_CODING
SBS Chr5 29086174 G-A Homo NON_SYNONYMOUS_CODING OsKitaake05g275100
SBS Chr6 16373322 G-T Hetero STOP_GAINED OsKitaake06g156500
SBS Chr6 21176625 T-A Hetero NON_SYNONYMOUS_CODING OsKitaake06g187900
SBS Chr6 21176626 T-A Hetero SYNONYMOUS_CODING
SBS Chr6 24803579 C-T Hetero INTRON
SBS Chr7 6332096 G-T Homo INTERGENIC
SBS Chr7 9533540 C-A Hetero INTERGENIC
SBS Chr7 10529822 C-T Homo INTERGENIC
SBS Chr7 15899158 G-A Hetero INTERGENIC
SBS Chr8 10971721 T-A Homo INTERGENIC
SBS Chr10 14325035 C-T Homo INTERGENIC
SBS Chr10 16204792 G-A Homo INTERGENIC
SBS Chr10 21671080 A-G Hetero INTRON
SBS Chr11 7076595 A-T Hetero INTERGENIC
SBS Chr11 7624368 G-T Hetero INTERGENIC
SBS Chr11 21382967 C-T Hetero INTERGENIC
SBS Chr11 21390065 C-A Hetero INTERGENIC

Deletions: 13

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr1 999102 999118 16 OsKitaake01g011500
Deletion Chr12 1091001 1114000 22999 2
Deletion Chr5 7128001 7248000 119999 8
Deletion Chr4 7502334 7502338 4
Deletion Chr12 8661077 8661079 2
Deletion Chr3 8841460 8841461 1
Deletion Chr10 9067555 9067562 7
Deletion Chr11 11588480 11588482 2
Deletion Chr10 12018001 12037000 18999
Deletion Chr9 12341007 12341011 4
Deletion Chr7 20409635 20409637 2
Deletion Chr9 21110001 21142000 31999 9
Deletion Chr4 22192035 22192036 1

Insertions: 1

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr11 11043632 11043635 2

Inversions: 4

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Inversion Chr1 3403316 3746422 OsKitaake01g045200
Inversion Chr1 3602096 3746424 OsKitaake01g048400
Inversion Chr6 16181717 16774240 OsKitaake06g158400
Inversion Chr6 16181722 16793573 OsKitaake06g158400

Translocations: 2

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes

Translocation Chr6 16774240 Chr2 37164064 2
Translocation Chr11 16887966 Chr2 37163923 OsKitaake02g398900

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	21616904	C-A	Homo	INTERGENIC
SBS	Chr1	28258026	C-A	Hetero	INTERGENIC
SBS	Chr2	13312260	C-T	Hetero	INTRON
SBS	Chr2	15564579	G-T	Hetero	INTERGENIC
SBS	Chr2	17764863	G-C	Hetero	UTR_5_PRIME
SBS	Chr3	16178337	C-A	Hetero	INTERGENIC
SBS	Chr3	22918122	T-A	Hetero	INTERGENIC
SBS	Chr3	23511412	C-A	Hetero	INTERGENIC
SBS	Chr3	34425196	C-T	Homo	INTERGENIC
SBS	Chr4	6081658	C-T	Hetero	INTERGENIC
SBS	Chr4	20612191	G-A	Homo	SYNONYMOUS_CODING
SBS	Chr4	21133405	C-T	Homo	INTRON
SBS	Chr4	24902003	T-G	Hetero	INTERGENIC
SBS	Chr4	27276516	C-T	Hetero	INTERGENIC
SBS	Chr4	28087754	A-G	Hetero	INTERGENIC
SBS	Chr5	7050707	T-C	Hetero	INTERGENIC
SBS	Chr5	22810573	C-T	Homo	INTERGENIC
SBS	Chr5	27817612	G-A	Homo	SYNONYMOUS_CODING
SBS	Chr5	29086174	G-A	Homo	NON_SYNONYMOUS_CODING	OsKitaake05g275100
SBS	Chr6	16373322	G-T	Hetero	STOP_GAINED	OsKitaake06g156500
SBS	Chr6	21176625	T-A	Hetero	NON_SYNONYMOUS_CODING	OsKitaake06g187900
SBS	Chr6	21176626	T-A	Hetero	SYNONYMOUS_CODING
SBS	Chr6	24803579	C-T	Hetero	INTRON
SBS	Chr7	6332096	G-T	Homo	INTERGENIC
SBS	Chr7	9533540	C-A	Hetero	INTERGENIC
SBS	Chr7	10529822	C-T	Homo	INTERGENIC
SBS	Chr7	15899158	G-A	Hetero	INTERGENIC
SBS	Chr8	10971721	T-A	Homo	INTERGENIC
SBS	Chr10	14325035	C-T	Homo	INTERGENIC
SBS	Chr10	16204792	G-A	Homo	INTERGENIC
SBS	Chr10	21671080	A-G	Hetero	INTRON
SBS	Chr11	7076595	A-T	Hetero	INTERGENIC
SBS	Chr11	7624368	G-T	Hetero	INTERGENIC
SBS	Chr11	21382967	C-T	Hetero	INTERGENIC
SBS	Chr11	21390065	C-A	Hetero	INTERGENIC

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr1	999102	999118	16	OsKitaake01g011500
Deletion	Chr12	1091001	1114000	22999	2
Deletion	Chr5	7128001	7248000	119999	8
Deletion	Chr4	7502334	7502338	4
Deletion	Chr12	8661077	8661079	2
Deletion	Chr3	8841460	8841461	1
Deletion	Chr10	9067555	9067562	7
Deletion	Chr11	11588480	11588482	2
Deletion	Chr10	12018001	12037000	18999
Deletion	Chr9	12341007	12341011	4
Deletion	Chr7	20409635	20409637	2
Deletion	Chr9	21110001	21142000	31999	9
Deletion	Chr4	22192035	22192036	1

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr1	3403316	3746422	OsKitaake01g045200
Inversion	Chr1	3602096	3746424	OsKitaake01g048400
Inversion	Chr6	16181717	16774240	OsKitaake06g158400
Inversion	Chr6	16181722	16793573	OsKitaake06g158400

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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

Position 2

Number of Genes

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes