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Mutant Information

Mutant Name	FN1286-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN1286-S Alignment File
Seed Availability	Yes [Order Seeds]
Phenotype	TO:0000326 (Leaf Color) = Normal TO:0000137 (Days to heading) = Normal (Between 75% and 125%) TO:0000346 (Tiller number) = Low (Between 25% and 74%) TO:0000430 (Germination Rate) = Normal (Between 75% and 125%) For more information, please see this phenotype file

Variant Information

Single base substitutions: 39

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 29879973 C-A Hetero INTERGENIC
SBS Chr1 30500100 T-A Hetero INTERGENIC
SBS Chr2 10587605 A-T Homo NON_SYNONYMOUS_CODING OsKitaake02g125100
SBS Chr2 16678139 T-G Homo INTERGENIC
SBS Chr2 25051186 C-T Homo INTERGENIC
SBS Chr2 35564573 G-A Hetero STOP_GAINED OsKitaake02g373600
SBS Chr3 8996852 A-G Hetero UTR_3_PRIME
SBS Chr3 19565220 T-C Hetero SYNONYMOUS_CODING
SBS Chr3 23184760 G-A Hetero INTERGENIC
SBS Chr3 25880891 G-A Hetero INTERGENIC
SBS Chr4 14314183 A-T Homo INTERGENIC
SBS Chr4 16377741 C-A Hetero INTERGENIC
SBS Chr4 26034422 T-G Hetero INTERGENIC
SBS Chr5 1896119 C-T Hetero NON_SYNONYMOUS_CODING OsKitaake05g021300
SBS Chr5 20595486 T-C Hetero INTERGENIC
SBS Chr6 3598037 G-A Hetero NON_SYNONYMOUS_CODING OsKitaake06g050000
SBS Chr6 3598040 T-A Hetero NON_SYNONYMOUS_CODING OsKitaake06g050000
SBS Chr6 4810700 A-G Hetero INTRON
SBS Chr6 21423117 C-T Hetero INTERGENIC
SBS Chr6 29460604 G-A Homo INTERGENIC
SBS Chr7 2969730 C-A Homo INTERGENIC
SBS Chr7 7372833 C-T Homo INTERGENIC
SBS Chr7 9799122 T-G Hetero INTERGENIC
SBS Chr7 17773681 G-A Hetero INTERGENIC
SBS Chr7 21006501 C-T Hetero INTERGENIC
SBS Chr7 29484551 A-G Hetero INTRON
SBS Chr8 5916193 C-A Homo INTRON
SBS Chr9 5312227 A-T Hetero INTERGENIC
SBS Chr9 12817220 G-A Homo INTRON
SBS Chr9 21984441 A-G Homo INTERGENIC
SBS Chr10 1218578 A-C Hetero INTERGENIC
SBS Chr10 17011267 G-A Hetero INTERGENIC
SBS Chr11 4876127 T-C Homo INTERGENIC
SBS Chr11 4876133 G-C Homo INTERGENIC
SBS Chr11 15230171 T-G Hetero INTERGENIC
SBS Chr11 19552850 G-A Hetero INTERGENIC
SBS Chr12 6029304 C-A Hetero INTERGENIC
SBS Chr12 12929061 C-G Hetero INTERGENIC
SBS Chr12 26017170 A-T Homo SYNONYMOUS_CODING

Deletions: 18

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr5 4991508 4991513 5
Deletion Chr1 5090001 5096000 5999 OsKitaake01g066900
Deletion Chr7 8940445 8940446 1
Deletion Chr1 9645001 9656000 10999 OsKitaake01g123400
Deletion Chr3 10218001 10279000 60999 8
Deletion Chr8 10537322 10537326 4
Deletion Chr4 10965153 10965156 3
Deletion Chr9 13331963 13331964 1
Deletion Chr12 14685401 14685405 4
Deletion Chr9 16606644 16606650 6
Deletion Chr8 17119649 17119651 2
Deletion Chr2 17310480 17310483 3
Deletion Chr4 23906932 23906943 11
Deletion Chr11 24238725 24238731 6
Deletion Chr4 28063886 28063890 4
Deletion Chr2 30412717 30412719 2
Deletion Chr1 31783065 31783068 3
Deletion Chr3 37209786 37209802 16

Insertions: 6

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr3 3924524 3924529 4
Insertion Chr6 30677758 30677761 2
Insertion Chr11 26692277 26692280 2
Insertion Chr3 6885482 6885485 2 OsKitaake03g097400
Insertion Chr9 10160983 10160987 3
Insertion Chr11 21352746 21352749 2

Inversions: 3

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Inversion Chr1 4252271 5090058 OsKitaake01g056800
Inversion Chr1 4252276 5095925 OsKitaake01g056800
Inversion Chr11 28390171 29067671

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	29879973	C-A	Hetero	INTERGENIC
SBS	Chr1	30500100	T-A	Hetero	INTERGENIC
SBS	Chr2	10587605	A-T	Homo	NON_SYNONYMOUS_CODING	OsKitaake02g125100
SBS	Chr2	16678139	T-G	Homo	INTERGENIC
SBS	Chr2	25051186	C-T	Homo	INTERGENIC
SBS	Chr2	35564573	G-A	Hetero	STOP_GAINED	OsKitaake02g373600
SBS	Chr3	8996852	A-G	Hetero	UTR_3_PRIME
SBS	Chr3	19565220	T-C	Hetero	SYNONYMOUS_CODING
SBS	Chr3	23184760	G-A	Hetero	INTERGENIC
SBS	Chr3	25880891	G-A	Hetero	INTERGENIC
SBS	Chr4	14314183	A-T	Homo	INTERGENIC
SBS	Chr4	16377741	C-A	Hetero	INTERGENIC
SBS	Chr4	26034422	T-G	Hetero	INTERGENIC
SBS	Chr5	1896119	C-T	Hetero	NON_SYNONYMOUS_CODING	OsKitaake05g021300
SBS	Chr5	20595486	T-C	Hetero	INTERGENIC
SBS	Chr6	3598037	G-A	Hetero	NON_SYNONYMOUS_CODING	OsKitaake06g050000
SBS	Chr6	3598040	T-A	Hetero	NON_SYNONYMOUS_CODING	OsKitaake06g050000
SBS	Chr6	4810700	A-G	Hetero	INTRON
SBS	Chr6	21423117	C-T	Hetero	INTERGENIC
SBS	Chr6	29460604	G-A	Homo	INTERGENIC
SBS	Chr7	2969730	C-A	Homo	INTERGENIC
SBS	Chr7	7372833	C-T	Homo	INTERGENIC
SBS	Chr7	9799122	T-G	Hetero	INTERGENIC
SBS	Chr7	17773681	G-A	Hetero	INTERGENIC
SBS	Chr7	21006501	C-T	Hetero	INTERGENIC
SBS	Chr7	29484551	A-G	Hetero	INTRON
SBS	Chr8	5916193	C-A	Homo	INTRON
SBS	Chr9	5312227	A-T	Hetero	INTERGENIC
SBS	Chr9	12817220	G-A	Homo	INTRON
SBS	Chr9	21984441	A-G	Homo	INTERGENIC
SBS	Chr10	1218578	A-C	Hetero	INTERGENIC
SBS	Chr10	17011267	G-A	Hetero	INTERGENIC
SBS	Chr11	4876127	T-C	Homo	INTERGENIC
SBS	Chr11	4876133	G-C	Homo	INTERGENIC
SBS	Chr11	15230171	T-G	Hetero	INTERGENIC
SBS	Chr11	19552850	G-A	Hetero	INTERGENIC
SBS	Chr12	6029304	C-A	Hetero	INTERGENIC
SBS	Chr12	12929061	C-G	Hetero	INTERGENIC
SBS	Chr12	26017170	A-T	Homo	SYNONYMOUS_CODING

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr5	4991508	4991513	5
Deletion	Chr1	5090001	5096000	5999	OsKitaake01g066900
Deletion	Chr7	8940445	8940446	1
Deletion	Chr1	9645001	9656000	10999	OsKitaake01g123400
Deletion	Chr3	10218001	10279000	60999	8
Deletion	Chr8	10537322	10537326	4
Deletion	Chr4	10965153	10965156	3
Deletion	Chr9	13331963	13331964	1
Deletion	Chr12	14685401	14685405	4
Deletion	Chr9	16606644	16606650	6
Deletion	Chr8	17119649	17119651	2
Deletion	Chr2	17310480	17310483	3
Deletion	Chr4	23906932	23906943	11
Deletion	Chr11	24238725	24238731	6
Deletion	Chr4	28063886	28063890	4
Deletion	Chr2	30412717	30412719	2
Deletion	Chr1	31783065	31783068	3
Deletion	Chr3	37209786	37209802	16

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr1	4252271	5090058	OsKitaake01g056800
Inversion	Chr1	4252276	5095925	OsKitaake01g056800
Inversion	Chr11	28390171	29067671

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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