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Mutant Information

Mutant Name	FN1476-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN1476-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) = Normal (Between 75% and 125%) TO:0000430 (Germination Rate) = Normal (Between 75% and 125%) 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 5397509 T-C Hetero INTERGENIC
SBS Chr1 12290769 C-G Hetero INTRON
SBS Chr2 121732 A-T Hetero INTERGENIC
SBS Chr2 1535511 C-A Hetero INTERGENIC
SBS Chr2 9773900 C-T Hetero INTRON
SBS Chr2 32881819 C-T Homo INTRON
SBS Chr3 10259284 T-G Homo INTERGENIC
SBS Chr3 14836230 G-T Homo INTERGENIC
SBS Chr3 18280009 G-C Homo INTERGENIC
SBS Chr3 18653039 G-A Homo INTERGENIC
SBS Chr4 4452189 G-C Hetero INTERGENIC
SBS Chr4 18656724 G-A Homo INTERGENIC
SBS Chr4 25631303 A-C Hetero INTRON
SBS Chr4 27406564 A-G Hetero INTERGENIC
SBS Chr4 28356034 C-A Hetero INTERGENIC
SBS Chr5 3303545 G-A Hetero INTERGENIC
SBS Chr5 10195603 T-C Hetero INTERGENIC
SBS Chr5 10325014 C-T Hetero INTERGENIC
SBS Chr5 14324363 G-A Hetero INTERGENIC
SBS Chr5 15764932 T-A Hetero INTRON
SBS Chr5 25006216 T-A Hetero INTERGENIC
SBS Chr6 2443194 A-T Hetero INTERGENIC
SBS Chr7 1226050 T-C Hetero INTERGENIC
SBS Chr7 10443541 C-T Hetero INTERGENIC
SBS Chr7 28399623 C-T Hetero INTERGENIC
SBS Chr8 4113781 C-T Hetero INTERGENIC
SBS Chr8 7345995 C-T Hetero INTERGENIC
SBS Chr8 8158619 C-T Hetero INTERGENIC
SBS Chr8 8972885 C-T Hetero INTERGENIC
SBS Chr8 8972894 T-A Hetero INTERGENIC
SBS Chr8 18670956 G-T Hetero INTRON
SBS Chr8 19561764 C-T Hetero NON_SYNONYMOUS_CODING OsKitaake08g143601
SBS Chr8 24956481 A-C Homo INTERGENIC
SBS Chr10 7777506 T-C Homo INTERGENIC
SBS Chr10 20894114 G-A Hetero NON_SYNONYMOUS_CODING OsKitaake10g160800
SBS Chr12 3377580 G-C Hetero INTERGENIC
SBS Chr12 15098838 G-A Hetero INTERGENIC
SBS Chr12 15853356 A-G Hetero INTERGENIC
SBS Chr12 16863657 T-C Hetero INTERGENIC
SBS Chr12 17293079 T-C Hetero SYNONYMOUS_CODING

Deletions: 123

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr3 84001 95000 10999 OsKitaake03g001200
Deletion Chr1 349001 385000 35999 OsKitaake01g005200
Deletion Chr2 598001 614000 15999 OsKitaake02g009000
Deletion Chr6 753001 776000 22999 2
Deletion Chr8 917001 946000 28999 2
Deletion Chr2 933001 940000 6999 OsKitaake02g013300
Deletion Chr3 1081001 1107000 25999 OsKitaake03g016901
Deletion Chr4 1525065 1525075 10
Deletion Chr2 1634001 1653000 18999 3
Deletion Chr11 1664001 1674000 9999 OsKitaake11g022200
Deletion Chr8 1670001 1694000 23999 2
Deletion Chr12 1738001 1749000 10999 OsKitaake12g026400
Deletion Chr6 1868001 1888000 19999 5
Deletion Chr6 1976001 1984000 7999 OsKitaake06g025000
Deletion Chr2 2046915 2046919 4
Deletion Chr2 2369001 2379000 9999 OsKitaake02g034800
Deletion Chr1 2614001 2633000 18999 OsKitaake01g033300
Deletion Chr9 2745018 2745019 1
Deletion Chr8 2924001 2941000 16999 2
Deletion Chr3 3002001 3025000 22999 6
Deletion Chr5 3402001 3415000 12999 OsKitaake05g041100
Deletion Chr2 3436001 3457000 20999 OsKitaake02g050200
Deletion Chr12 3727170 3727174 4
Deletion Chr5 3744001 3750000 5999 OsKitaake05g044900
Deletion Chr6 4090001 4102000 11999 OsKitaake06g057500
Deletion Chr10 4146503 4146504 1
Deletion Chr2 4734001 4741000 6999 OsKitaake02g065500
Deletion Chr4 5086001 5097000 10999 OsKitaake04g024100
Deletion Chr2 5230001 5242000 11999 OsKitaake02g072000
Deletion Chr2 5810001 5822000 11999 OsKitaake02g080100
Deletion Chr3 5893001 5917000 23999 3
Deletion Chr5 5932001 5941000 8999
Deletion Chr7 5985001 6005000 19999 OsKitaake07g072200
Deletion Chr4 6003001 6010000 6999 OsKitaake04g030100
Deletion Chr6 6018001 6037000 18999 8
Deletion Chr2 6212001 6232000 19999 3
Deletion Chr12 6814001 6846000 31999 5
Deletion Chr12 7151001 7162000 10999 OsKitaake12g080100
Deletion Chr12 7198001 7227000 28999 2
Deletion Chr11 7473001 7484000 10999 OsKitaake11g084366
Deletion Chr9 7980001 7998000 17999 OsKitaake09g045100
Deletion Chr2 8601001 8617000 15999 OsKitaake02g109400
Deletion Chr5 8646001 8655000 8999 OsKitaake05g082400
Deletion Chr10 8674720 8675052 332
Deletion Chr4 8938001 8950000 11999 OsKitaake04g046100
Deletion Chr11 9474001 9500000 25999 3
Deletion Chr1 9646001 9656000 9999 OsKitaake01g123400
Deletion Chr10 10484001 10500000 15999 OsKitaake10g061300
Deletion Chr2 10500001 10533000 32999 3
Deletion Chr12 10937001 10960000 22999 2
Deletion Chr3 11229001 11251000 21999 2
Deletion Chr3 12581154 12581162 8
Deletion Chr3 12821001 12832000 10999 OsKitaake03g172500
Deletion Chr10 13056001 13081000 24999 3
Deletion Chr6 13354001 13366000 11999 OsKitaake06g141100
Deletion Chr9 13503038 13503045 7
Deletion Chr10 14167001 14187000 19999 4
Deletion Chr4 14175001 14184000 8999 OsKitaake04g067900
Deletion Chr8 14377001 14385000 7999 OsKitaake08g112900
Deletion Chr10 14622001 14632000 9999 2
Deletion Chr1 14677001 14695000 17999 OsKitaake01g166200
Deletion Chr9 14989001 15005000 15999
Deletion Chr10 15181001 15193000 11999 3
Deletion Chr7 15552001 15580000 27999 4
Deletion Chr3 16706001 16718000 11999 OsKitaake03g210400
Deletion Chr5 16786001 16806000 19999 OsKitaake05g128600
Deletion Chr9 16959001 16978000 18999 OsKitaake09g125700
Deletion Chr12 17160001 17176000 15999 2
Deletion Chr4 17406001 17435000 28999 5
Deletion Chr4 17639001 17650000 10999 OsKitaake04g088300
Deletion Chr7 17712001 17740000 27999 2
Deletion Chr5 17901001 17908000 6999 OsKitaake05g138700
Deletion Chr6 17906001 17916000 9999 OsKitaake06g164800
Deletion Chr6 18337001 18379000 41999 OsKitaake06g168100
Deletion Chr10 18525001 18536000 10999 OsKitaake10g131700
Deletion Chr7 18526001 18538000 11999 OsKitaake07g150700
Deletion Chr8 18669453 18669455 2
Deletion Chr2 18689001 18706000 16999 OsKitaake02g184000
Deletion Chr5 19103001 19110000 6999 OsKitaake05g149300
Deletion Chr2 19945001 19954000 8999 OsKitaake02g194300
Deletion Chr2 20550466 20550788 322
Deletion Chr2 20767001 20811000 43999 2
Deletion Chr9 21389157 21389180 23
Deletion Chr3 21408131 21408137 6
Deletion Chr5 21987001 21998000 10999 5
Deletion Chr4 22736001 22755000 18999 7
Deletion Chr7 22915001 22926000 10999 OsKitaake07g197300
Deletion Chr3 22981001 22989000 7999
Deletion Chr1 23739001 23781000 41999 3
Deletion Chr6 23787001 23811000 23999 5
Deletion Chr3 24060001 24075000 14999 OsKitaake03g257300
Deletion Chr2 24406001 24431000 24999
Deletion Chr3 25212001 25245000 32999 2
Deletion Chr2 25469001 25480000 10999 2
Deletion Chr12 25743001 25753000 9999
Deletion Chr6 25995001 26012000 16999 2
Deletion Chr12 26723001 26734000 10999 OsKitaake12g222100
Deletion Chr6 26786001 26793000 6999 OsKitaake06g239800
Deletion Chr3 26991223 26991224 1
Deletion Chr7 27172043 27172047 4
Deletion Chr3 27630380 27630382 2
Deletion Chr5 27657001 27663000 5999 OsKitaake05g252600
Deletion Chr2 27667001 27691000 23999 3
Deletion Chr7 27790001 27802000 11999 OsKitaake07g259700
Deletion Chr6 27915001 27936000 20999 OsKitaake06g253400
Deletion Chr3 28578001 28599000 20999 OsKitaake03g296500
Deletion Chr7 28876001 28897000 20999 3
Deletion Chr1 29252001 29260000 7999 OsKitaake01g285100
Deletion Chr7 29518001 29529000 10999 2
Deletion Chr4 29871001 29884000 12999 OsKitaake04g229500
Deletion Chr1 30446001 30466000 19999 OsKitaake01g301100
Deletion Chr3 30871001 30882000 10999 2
Deletion Chr6 30977001 30988000 10999 2
Deletion Chr3 31418001 31427000 8999 OsKitaake03g331400
Deletion Chr4 31794001 31805000 10999
Deletion Chr1 32398001 32407000 8999 2
Deletion Chr2 33317001 33329000 11999 2
Deletion Chr3 34117001 34129000 11999 OsKitaake03g368700
Deletion Chr2 34165001 34191000 25999 4
Deletion Chr3 35337001 35344000 6999 OsKitaake03g387600
Deletion Chr3 36387001 36397000 9999 3
Deletion Chr1 41000001 41017000 16999 2
Deletion Chr1 44229001 44239000 9999 OsKitaake01g494300

Insertions: 3

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr3 15986072 15986075 2
Insertion Chr8 9052760 9052765 4
Insertion Chr12 16611174 16611177 2

Inversions: 2

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Inversion Chr4 26941851 27365751 2
Inversion Chr4 27122933 27277993 OsKitaake04g197300

Translocations: 2

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes

Translocation Chr12 292000 Chr5 15167687
Translocation Chr12 292002 Chr5 15167878

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	5397509	T-C	Hetero	INTERGENIC
SBS	Chr1	12290769	C-G	Hetero	INTRON
SBS	Chr2	121732	A-T	Hetero	INTERGENIC
SBS	Chr2	1535511	C-A	Hetero	INTERGENIC
SBS	Chr2	9773900	C-T	Hetero	INTRON
SBS	Chr2	32881819	C-T	Homo	INTRON
SBS	Chr3	10259284	T-G	Homo	INTERGENIC
SBS	Chr3	14836230	G-T	Homo	INTERGENIC
SBS	Chr3	18280009	G-C	Homo	INTERGENIC
SBS	Chr3	18653039	G-A	Homo	INTERGENIC
SBS	Chr4	4452189	G-C	Hetero	INTERGENIC
SBS	Chr4	18656724	G-A	Homo	INTERGENIC
SBS	Chr4	25631303	A-C	Hetero	INTRON
SBS	Chr4	27406564	A-G	Hetero	INTERGENIC
SBS	Chr4	28356034	C-A	Hetero	INTERGENIC
SBS	Chr5	3303545	G-A	Hetero	INTERGENIC
SBS	Chr5	10195603	T-C	Hetero	INTERGENIC
SBS	Chr5	10325014	C-T	Hetero	INTERGENIC
SBS	Chr5	14324363	G-A	Hetero	INTERGENIC
SBS	Chr5	15764932	T-A	Hetero	INTRON
SBS	Chr5	25006216	T-A	Hetero	INTERGENIC
SBS	Chr6	2443194	A-T	Hetero	INTERGENIC
SBS	Chr7	1226050	T-C	Hetero	INTERGENIC
SBS	Chr7	10443541	C-T	Hetero	INTERGENIC
SBS	Chr7	28399623	C-T	Hetero	INTERGENIC
SBS	Chr8	4113781	C-T	Hetero	INTERGENIC
SBS	Chr8	7345995	C-T	Hetero	INTERGENIC
SBS	Chr8	8158619	C-T	Hetero	INTERGENIC
SBS	Chr8	8972885	C-T	Hetero	INTERGENIC
SBS	Chr8	8972894	T-A	Hetero	INTERGENIC
SBS	Chr8	18670956	G-T	Hetero	INTRON
SBS	Chr8	19561764	C-T	Hetero	NON_SYNONYMOUS_CODING	OsKitaake08g143601
SBS	Chr8	24956481	A-C	Homo	INTERGENIC
SBS	Chr10	7777506	T-C	Homo	INTERGENIC
SBS	Chr10	20894114	G-A	Hetero	NON_SYNONYMOUS_CODING	OsKitaake10g160800
SBS	Chr12	3377580	G-C	Hetero	INTERGENIC
SBS	Chr12	15098838	G-A	Hetero	INTERGENIC
SBS	Chr12	15853356	A-G	Hetero	INTERGENIC
SBS	Chr12	16863657	T-C	Hetero	INTERGENIC
SBS	Chr12	17293079	T-C	Hetero	SYNONYMOUS_CODING

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr3	84001	95000	10999	OsKitaake03g001200
Deletion	Chr1	349001	385000	35999	OsKitaake01g005200
Deletion	Chr2	598001	614000	15999	OsKitaake02g009000
Deletion	Chr6	753001	776000	22999	2
Deletion	Chr8	917001	946000	28999	2
Deletion	Chr2	933001	940000	6999	OsKitaake02g013300
Deletion	Chr3	1081001	1107000	25999	OsKitaake03g016901
Deletion	Chr4	1525065	1525075	10
Deletion	Chr2	1634001	1653000	18999	3
Deletion	Chr11	1664001	1674000	9999	OsKitaake11g022200
Deletion	Chr8	1670001	1694000	23999	2
Deletion	Chr12	1738001	1749000	10999	OsKitaake12g026400
Deletion	Chr6	1868001	1888000	19999	5
Deletion	Chr6	1976001	1984000	7999	OsKitaake06g025000
Deletion	Chr2	2046915	2046919	4
Deletion	Chr2	2369001	2379000	9999	OsKitaake02g034800
Deletion	Chr1	2614001	2633000	18999	OsKitaake01g033300
Deletion	Chr9	2745018	2745019	1
Deletion	Chr8	2924001	2941000	16999	2
Deletion	Chr3	3002001	3025000	22999	6
Deletion	Chr5	3402001	3415000	12999	OsKitaake05g041100
Deletion	Chr2	3436001	3457000	20999	OsKitaake02g050200
Deletion	Chr12	3727170	3727174	4
Deletion	Chr5	3744001	3750000	5999	OsKitaake05g044900
Deletion	Chr6	4090001	4102000	11999	OsKitaake06g057500
Deletion	Chr10	4146503	4146504	1
Deletion	Chr2	4734001	4741000	6999	OsKitaake02g065500
Deletion	Chr4	5086001	5097000	10999	OsKitaake04g024100
Deletion	Chr2	5230001	5242000	11999	OsKitaake02g072000
Deletion	Chr2	5810001	5822000	11999	OsKitaake02g080100
Deletion	Chr3	5893001	5917000	23999	3
Deletion	Chr5	5932001	5941000	8999
Deletion	Chr7	5985001	6005000	19999	OsKitaake07g072200
Deletion	Chr4	6003001	6010000	6999	OsKitaake04g030100
Deletion	Chr6	6018001	6037000	18999	8
Deletion	Chr2	6212001	6232000	19999	3
Deletion	Chr12	6814001	6846000	31999	5
Deletion	Chr12	7151001	7162000	10999	OsKitaake12g080100
Deletion	Chr12	7198001	7227000	28999	2
Deletion	Chr11	7473001	7484000	10999	OsKitaake11g084366
Deletion	Chr9	7980001	7998000	17999	OsKitaake09g045100
Deletion	Chr2	8601001	8617000	15999	OsKitaake02g109400
Deletion	Chr5	8646001	8655000	8999	OsKitaake05g082400
Deletion	Chr10	8674720	8675052	332
Deletion	Chr4	8938001	8950000	11999	OsKitaake04g046100
Deletion	Chr11	9474001	9500000	25999	3
Deletion	Chr1	9646001	9656000	9999	OsKitaake01g123400
Deletion	Chr10	10484001	10500000	15999	OsKitaake10g061300
Deletion	Chr2	10500001	10533000	32999	3
Deletion	Chr12	10937001	10960000	22999	2
Deletion	Chr3	11229001	11251000	21999	2
Deletion	Chr3	12581154	12581162	8
Deletion	Chr3	12821001	12832000	10999	OsKitaake03g172500
Deletion	Chr10	13056001	13081000	24999	3
Deletion	Chr6	13354001	13366000	11999	OsKitaake06g141100
Deletion	Chr9	13503038	13503045	7
Deletion	Chr10	14167001	14187000	19999	4
Deletion	Chr4	14175001	14184000	8999	OsKitaake04g067900
Deletion	Chr8	14377001	14385000	7999	OsKitaake08g112900
Deletion	Chr10	14622001	14632000	9999	2
Deletion	Chr1	14677001	14695000	17999	OsKitaake01g166200
Deletion	Chr9	14989001	15005000	15999
Deletion	Chr10	15181001	15193000	11999	3
Deletion	Chr7	15552001	15580000	27999	4
Deletion	Chr3	16706001	16718000	11999	OsKitaake03g210400
Deletion	Chr5	16786001	16806000	19999	OsKitaake05g128600
Deletion	Chr9	16959001	16978000	18999	OsKitaake09g125700
Deletion	Chr12	17160001	17176000	15999	2
Deletion	Chr4	17406001	17435000	28999	5
Deletion	Chr4	17639001	17650000	10999	OsKitaake04g088300
Deletion	Chr7	17712001	17740000	27999	2
Deletion	Chr5	17901001	17908000	6999	OsKitaake05g138700
Deletion	Chr6	17906001	17916000	9999	OsKitaake06g164800
Deletion	Chr6	18337001	18379000	41999	OsKitaake06g168100
Deletion	Chr10	18525001	18536000	10999	OsKitaake10g131700
Deletion	Chr7	18526001	18538000	11999	OsKitaake07g150700
Deletion	Chr8	18669453	18669455	2
Deletion	Chr2	18689001	18706000	16999	OsKitaake02g184000
Deletion	Chr5	19103001	19110000	6999	OsKitaake05g149300
Deletion	Chr2	19945001	19954000	8999	OsKitaake02g194300
Deletion	Chr2	20550466	20550788	322
Deletion	Chr2	20767001	20811000	43999	2
Deletion	Chr9	21389157	21389180	23
Deletion	Chr3	21408131	21408137	6
Deletion	Chr5	21987001	21998000	10999	5
Deletion	Chr4	22736001	22755000	18999	7
Deletion	Chr7	22915001	22926000	10999	OsKitaake07g197300
Deletion	Chr3	22981001	22989000	7999
Deletion	Chr1	23739001	23781000	41999	3
Deletion	Chr6	23787001	23811000	23999	5
Deletion	Chr3	24060001	24075000	14999	OsKitaake03g257300
Deletion	Chr2	24406001	24431000	24999
Deletion	Chr3	25212001	25245000	32999	2
Deletion	Chr2	25469001	25480000	10999	2
Deletion	Chr12	25743001	25753000	9999
Deletion	Chr6	25995001	26012000	16999	2
Deletion	Chr12	26723001	26734000	10999	OsKitaake12g222100
Deletion	Chr6	26786001	26793000	6999	OsKitaake06g239800
Deletion	Chr3	26991223	26991224	1
Deletion	Chr7	27172043	27172047	4
Deletion	Chr3	27630380	27630382	2
Deletion	Chr5	27657001	27663000	5999	OsKitaake05g252600
Deletion	Chr2	27667001	27691000	23999	3
Deletion	Chr7	27790001	27802000	11999	OsKitaake07g259700
Deletion	Chr6	27915001	27936000	20999	OsKitaake06g253400
Deletion	Chr3	28578001	28599000	20999	OsKitaake03g296500
Deletion	Chr7	28876001	28897000	20999	3
Deletion	Chr1	29252001	29260000	7999	OsKitaake01g285100
Deletion	Chr7	29518001	29529000	10999	2
Deletion	Chr4	29871001	29884000	12999	OsKitaake04g229500
Deletion	Chr1	30446001	30466000	19999	OsKitaake01g301100
Deletion	Chr3	30871001	30882000	10999	2
Deletion	Chr6	30977001	30988000	10999	2
Deletion	Chr3	31418001	31427000	8999	OsKitaake03g331400
Deletion	Chr4	31794001	31805000	10999
Deletion	Chr1	32398001	32407000	8999	2
Deletion	Chr2	33317001	33329000	11999	2
Deletion	Chr3	34117001	34129000	11999	OsKitaake03g368700
Deletion	Chr2	34165001	34191000	25999	4
Deletion	Chr3	35337001	35344000	6999	OsKitaake03g387600
Deletion	Chr3	36387001	36397000	9999	3
Deletion	Chr1	41000001	41017000	16999	2
Deletion	Chr1	44229001	44239000	9999	OsKitaake01g494300

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr4	26941851	27365751	2
Inversion	Chr4	27122933	27277993	OsKitaake04g197300

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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