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Mutant Information

Mutant Name	FN1401-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN1401-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: 42

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 7890355 C-T Hetero INTERGENIC
SBS Chr1 8962062 G-T Hetero INTERGENIC
SBS Chr1 16113507 T-G Hetero INTERGENIC
SBS Chr1 20756696 A-G Hetero INTERGENIC
SBS Chr1 30337034 G-A Homo INTERGENIC
SBS Chr1 43461421 A-C Hetero SYNONYMOUS_CODING
SBS Chr2 6674102 T-C Homo INTERGENIC
SBS Chr2 23766973 G-A Homo INTERGENIC
SBS Chr2 31850683 T-C Hetero INTERGENIC
SBS Chr3 15634415 T-A Hetero INTERGENIC
SBS Chr3 16193426 G-A Hetero INTRON
SBS Chr3 19740483 C-A Hetero INTERGENIC
SBS Chr3 29648247 C-A Hetero INTRON
SBS Chr4 5421552 G-A Homo INTERGENIC
SBS Chr4 35571394 C-A Hetero INTERGENIC
SBS Chr5 13780635 T-C Hetero INTRON
SBS Chr5 27515528 C-T Hetero INTERGENIC
SBS Chr6 5519608 A-T Hetero INTERGENIC
SBS Chr7 11708204 T-A Hetero INTRON
SBS Chr7 14487854 T-C Hetero INTERGENIC
SBS Chr8 6192787 G-A Hetero INTERGENIC
SBS Chr8 7703909 A-T Homo INTERGENIC
SBS Chr8 19004845 C-T Hetero INTERGENIC
SBS Chr8 21055528 A-G Hetero INTERGENIC
SBS Chr9 4017730 C-G Hetero INTERGENIC
SBS Chr9 6934665 C-T Hetero INTERGENIC
SBS Chr9 9402218 C-G Hetero INTERGENIC
SBS Chr9 11480269 C-T Hetero INTERGENIC
SBS Chr9 16075601 G-A Hetero INTERGENIC
SBS Chr9 22052812 C-A Hetero INTERGENIC
SBS Chr10 8471542 G-A Homo INTERGENIC
SBS Chr10 12301961 G-A Hetero INTERGENIC
SBS Chr10 16317209 C-T Hetero INTRON
SBS Chr11 12955930 C-A Hetero INTERGENIC
SBS Chr11 14413901 C-A Hetero INTERGENIC
SBS Chr12 3554945 G-T Hetero INTERGENIC
SBS Chr12 6926897 A-T Hetero INTERGENIC
SBS Chr12 11462003 A-C Hetero INTERGENIC
SBS Chr12 14204371 T-A Hetero INTERGENIC
SBS Chr12 17881318 G-A Hetero INTRON
SBS Chr12 20319188 G-C Hetero INTERGENIC
SBS Chr12 23906510 C-G Hetero INTRON

Deletions: 23

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr12 1485718 1486109 391
Deletion Chr10 1578718 1578723 5
Deletion Chr3 3802061 3802070 9
Deletion Chr10 5241655 5241660 5 OsKitaake10g037500
Deletion Chr3 6094001 6106000 11999 OsKitaake03g087400
Deletion Chr9 9329188 9329203 15
Deletion Chr8 9896868 9896880 12
Deletion Chr11 11275784 11275785 1
Deletion Chr1 13458001 13471000 12999 2
Deletion Chr3 16512602 16512608 6
Deletion Chr7 18617267 18617274 7
Deletion Chr12 21286001 21326000 39999 5
Deletion Chr8 21296001 21309000 12999 OsKitaake08g159900
Deletion Chr12 21332001 21458000 125999 6
Deletion Chr2 22322472 22322475 3
Deletion Chr1 23255001 23272000 16999 OsKitaake01g222400
Deletion Chr1 25579020 25579021 1
Deletion Chr7 25890317 25890321 4
Deletion Chr1 26992357 26992358 1
Deletion Chr8 28506548 28506550 2
Deletion Chr3 28586001 28594000 7999 OsKitaake03g296500
Deletion Chr2 36446264 36446272 8
Deletion Chr1 42303001 42316000 12999 OsKitaake01g466400

Insertions: 7

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr1 5565457 5565460 2
Insertion Chr3 10051279 10051281 1
Insertion Chr7 5964366 5964369 2
Insertion Chr7 18906329 18906332 2
Insertion Chr8 15138728 15138731 2 OsKitaake08g118400
Insertion Chr11 28951935 28951938 2
Insertion Chr2 22105695 22105697 1

Inversions: 2

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Inversion Chr12 12519689 13369324 OsKitaake12g111100
Inversion Chr12 12519691 13369336 OsKitaake12g111100

Translocations: 1

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes

Translocation Chr8 8405700 Chr3 10399010

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	7890355	C-T	Hetero	INTERGENIC
SBS	Chr1	8962062	G-T	Hetero	INTERGENIC
SBS	Chr1	16113507	T-G	Hetero	INTERGENIC
SBS	Chr1	20756696	A-G	Hetero	INTERGENIC
SBS	Chr1	30337034	G-A	Homo	INTERGENIC
SBS	Chr1	43461421	A-C	Hetero	SYNONYMOUS_CODING
SBS	Chr2	6674102	T-C	Homo	INTERGENIC
SBS	Chr2	23766973	G-A	Homo	INTERGENIC
SBS	Chr2	31850683	T-C	Hetero	INTERGENIC
SBS	Chr3	15634415	T-A	Hetero	INTERGENIC
SBS	Chr3	16193426	G-A	Hetero	INTRON
SBS	Chr3	19740483	C-A	Hetero	INTERGENIC
SBS	Chr3	29648247	C-A	Hetero	INTRON
SBS	Chr4	5421552	G-A	Homo	INTERGENIC
SBS	Chr4	35571394	C-A	Hetero	INTERGENIC
SBS	Chr5	13780635	T-C	Hetero	INTRON
SBS	Chr5	27515528	C-T	Hetero	INTERGENIC
SBS	Chr6	5519608	A-T	Hetero	INTERGENIC
SBS	Chr7	11708204	T-A	Hetero	INTRON
SBS	Chr7	14487854	T-C	Hetero	INTERGENIC
SBS	Chr8	6192787	G-A	Hetero	INTERGENIC
SBS	Chr8	7703909	A-T	Homo	INTERGENIC
SBS	Chr8	19004845	C-T	Hetero	INTERGENIC
SBS	Chr8	21055528	A-G	Hetero	INTERGENIC
SBS	Chr9	4017730	C-G	Hetero	INTERGENIC
SBS	Chr9	6934665	C-T	Hetero	INTERGENIC
SBS	Chr9	9402218	C-G	Hetero	INTERGENIC
SBS	Chr9	11480269	C-T	Hetero	INTERGENIC
SBS	Chr9	16075601	G-A	Hetero	INTERGENIC
SBS	Chr9	22052812	C-A	Hetero	INTERGENIC
SBS	Chr10	8471542	G-A	Homo	INTERGENIC
SBS	Chr10	12301961	G-A	Hetero	INTERGENIC
SBS	Chr10	16317209	C-T	Hetero	INTRON
SBS	Chr11	12955930	C-A	Hetero	INTERGENIC
SBS	Chr11	14413901	C-A	Hetero	INTERGENIC
SBS	Chr12	3554945	G-T	Hetero	INTERGENIC
SBS	Chr12	6926897	A-T	Hetero	INTERGENIC
SBS	Chr12	11462003	A-C	Hetero	INTERGENIC
SBS	Chr12	14204371	T-A	Hetero	INTERGENIC
SBS	Chr12	17881318	G-A	Hetero	INTRON
SBS	Chr12	20319188	G-C	Hetero	INTERGENIC
SBS	Chr12	23906510	C-G	Hetero	INTRON

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr12	1485718	1486109	391
Deletion	Chr10	1578718	1578723	5
Deletion	Chr3	3802061	3802070	9
Deletion	Chr10	5241655	5241660	5	OsKitaake10g037500
Deletion	Chr3	6094001	6106000	11999	OsKitaake03g087400
Deletion	Chr9	9329188	9329203	15
Deletion	Chr8	9896868	9896880	12
Deletion	Chr11	11275784	11275785	1
Deletion	Chr1	13458001	13471000	12999	2
Deletion	Chr3	16512602	16512608	6
Deletion	Chr7	18617267	18617274	7
Deletion	Chr12	21286001	21326000	39999	5
Deletion	Chr8	21296001	21309000	12999	OsKitaake08g159900
Deletion	Chr12	21332001	21458000	125999	6
Deletion	Chr2	22322472	22322475	3
Deletion	Chr1	23255001	23272000	16999	OsKitaake01g222400
Deletion	Chr1	25579020	25579021	1
Deletion	Chr7	25890317	25890321	4
Deletion	Chr1	26992357	26992358	1
Deletion	Chr8	28506548	28506550	2
Deletion	Chr3	28586001	28594000	7999	OsKitaake03g296500
Deletion	Chr2	36446264	36446272	8
Deletion	Chr1	42303001	42316000	12999	OsKitaake01g466400

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr12	12519689	13369324	OsKitaake12g111100
Inversion	Chr12	12519691	13369336	OsKitaake12g111100

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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