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Mutant Information

Mutant Name	FN1402-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN1402-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) = High (Between 126% and 175%) TO:0000430 (Germination Rate) = Normal (Between 75% and 125%) For more information, please see this phenotype file

Variant Information

Single base substitutions: 47

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 1434964 C-A Homo INTERGENIC
SBS Chr1 10061883 C-T Hetero INTERGENIC
SBS Chr1 23037737 C-T Hetero INTRON
SBS Chr1 25601043 T-C Homo INTERGENIC
SBS Chr1 28665380 C-T Hetero INTERGENIC
SBS Chr2 19125300 T-C Hetero INTERGENIC
SBS Chr3 1014793 C-T Hetero INTERGENIC
SBS Chr3 4059297 T-C Hetero INTRON
SBS Chr3 8283498 C-G Hetero INTERGENIC
SBS Chr3 16546623 T-C Hetero INTERGENIC
SBS Chr3 19230931 G-A Hetero INTERGENIC
SBS Chr3 23642776 T-C Hetero UTR_3_PRIME
SBS Chr3 25682776 A-T Hetero INTERGENIC
SBS Chr3 25683964 G-T Hetero INTERGENIC
SBS Chr3 25683965 G-A Hetero INTERGENIC
SBS Chr3 33644885 C-T Homo INTERGENIC
SBS Chr4 4130722 T-C Hetero INTERGENIC
SBS Chr4 9219361 T-G Homo INTRON
SBS Chr4 21207096 G-T Homo INTERGENIC
SBS Chr5 6053087 A-G Hetero INTERGENIC
SBS Chr5 17095984 T-C Hetero INTERGENIC
SBS Chr5 21037572 C-A Homo SYNONYMOUS_CODING
SBS Chr6 10815512 C-T Hetero INTERGENIC
SBS Chr6 13065390 A-T Hetero INTERGENIC
SBS Chr6 23113218 T-C Homo INTERGENIC
SBS Chr6 24865316 G-T Hetero INTERGENIC
SBS Chr7 12722982 A-C Hetero INTERGENIC
SBS Chr7 13608677 C-T Hetero INTERGENIC
SBS Chr8 1643633 C-T Hetero INTERGENIC
SBS Chr8 3235964 T-A Hetero INTERGENIC
SBS Chr8 12910948 G-A Homo SYNONYMOUS_CODING
SBS Chr8 18610853 T-A Homo INTRON
SBS Chr8 18610854 G-T Homo INTRON
SBS Chr9 2825125 G-A Hetero INTERGENIC
SBS Chr9 2825127 T-A Hetero INTERGENIC
SBS Chr9 16183362 G-A Hetero SYNONYMOUS_CODING
SBS Chr10 17891465 T-C Hetero INTERGENIC
SBS Chr10 19712447 C-T Homo NON_SYNONYMOUS_CODING OsKitaake10g146000
SBS Chr11 2513903 T-A Hetero INTERGENIC
SBS Chr11 14053509 A-C Homo INTRON
SBS Chr11 14123548 T-A Homo INTERGENIC
SBS Chr11 14415771 G-A Homo INTERGENIC
SBS Chr11 17563136 T-C Hetero INTERGENIC
SBS Chr11 21610197 T-A Hetero NON_SYNONYMOUS_CODING OsKitaake11g170900
SBS Chr11 29196733 G-A Hetero INTERGENIC
SBS Chr12 1981510 C-T Homo INTERGENIC
SBS Chr12 9814137 C-T Hetero INTERGENIC

Deletions: 21

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr6 18326 18327 1
Deletion Chr7 5354544 5354545 1
Deletion Chr8 5432526 5432528 2
Deletion Chr5 5510289 5510291 2
Deletion Chr4 6974092 6974094 2
Deletion Chr10 8269928 8269930 2
Deletion Chr1 9648001 9658000 9999 OsKitaake01g123400
Deletion Chr8 10299652 10299654 2
Deletion Chr1 13460001 13470000 9999 OsKitaake01g156600
Deletion Chr10 13789365 13789367 2
Deletion Chr3 15097267 15097271 4
Deletion Chr1 17628168 17628170 2
Deletion Chr10 18690106 18690107 1
Deletion Chr4 19438001 19447000 8999 OsKitaake04g099601
Deletion Chr2 22296239 22296241 2
Deletion Chr3 22837223 22837225 2
Deletion Chr10 23243098 23243099 1
Deletion Chr6 25022333 25022341 8
Deletion Chr6 28875571 28875573 2
Deletion Chr1 34725538 34725551 13 OsKitaake01g364900
Deletion Chr3 37587685 37587687 2

Insertions: 7

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr1 37365555 37365557 1
Insertion Chr5 22076907 22076910 2
Insertion Chr8 4831893 4831897 3
Insertion Chr10 13525053 13525056 2
Insertion Chr10 16315795 16315798 2
Insertion Chr10 19255675 19255678 2
Insertion Chr4 2728023 2728026 2

Inversions: 4

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Inversion Chr8 2417562 3315486 2
Inversion Chr8 18089692 18611758 2
Inversion Chr1 23039948 23080154 OsKitaake01g219500
Inversion Chr1 23040016 23080182 OsKitaake01g219500

Translocations: 2

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes

Translocation Chr4 10438163 Chr3 27446181 OsKitaake04g055550
Translocation Chr4 10439324 Chr3 27446199

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	1434964	C-A	Homo	INTERGENIC
SBS	Chr1	10061883	C-T	Hetero	INTERGENIC
SBS	Chr1	23037737	C-T	Hetero	INTRON
SBS	Chr1	25601043	T-C	Homo	INTERGENIC
SBS	Chr1	28665380	C-T	Hetero	INTERGENIC
SBS	Chr2	19125300	T-C	Hetero	INTERGENIC
SBS	Chr3	1014793	C-T	Hetero	INTERGENIC
SBS	Chr3	4059297	T-C	Hetero	INTRON
SBS	Chr3	8283498	C-G	Hetero	INTERGENIC
SBS	Chr3	16546623	T-C	Hetero	INTERGENIC
SBS	Chr3	19230931	G-A	Hetero	INTERGENIC
SBS	Chr3	23642776	T-C	Hetero	UTR_3_PRIME
SBS	Chr3	25682776	A-T	Hetero	INTERGENIC
SBS	Chr3	25683964	G-T	Hetero	INTERGENIC
SBS	Chr3	25683965	G-A	Hetero	INTERGENIC
SBS	Chr3	33644885	C-T	Homo	INTERGENIC
SBS	Chr4	4130722	T-C	Hetero	INTERGENIC
SBS	Chr4	9219361	T-G	Homo	INTRON
SBS	Chr4	21207096	G-T	Homo	INTERGENIC
SBS	Chr5	6053087	A-G	Hetero	INTERGENIC
SBS	Chr5	17095984	T-C	Hetero	INTERGENIC
SBS	Chr5	21037572	C-A	Homo	SYNONYMOUS_CODING
SBS	Chr6	10815512	C-T	Hetero	INTERGENIC
SBS	Chr6	13065390	A-T	Hetero	INTERGENIC
SBS	Chr6	23113218	T-C	Homo	INTERGENIC
SBS	Chr6	24865316	G-T	Hetero	INTERGENIC
SBS	Chr7	12722982	A-C	Hetero	INTERGENIC
SBS	Chr7	13608677	C-T	Hetero	INTERGENIC
SBS	Chr8	1643633	C-T	Hetero	INTERGENIC
SBS	Chr8	3235964	T-A	Hetero	INTERGENIC
SBS	Chr8	12910948	G-A	Homo	SYNONYMOUS_CODING
SBS	Chr8	18610853	T-A	Homo	INTRON
SBS	Chr8	18610854	G-T	Homo	INTRON
SBS	Chr9	2825125	G-A	Hetero	INTERGENIC
SBS	Chr9	2825127	T-A	Hetero	INTERGENIC
SBS	Chr9	16183362	G-A	Hetero	SYNONYMOUS_CODING
SBS	Chr10	17891465	T-C	Hetero	INTERGENIC
SBS	Chr10	19712447	C-T	Homo	NON_SYNONYMOUS_CODING	OsKitaake10g146000
SBS	Chr11	2513903	T-A	Hetero	INTERGENIC
SBS	Chr11	14053509	A-C	Homo	INTRON
SBS	Chr11	14123548	T-A	Homo	INTERGENIC
SBS	Chr11	14415771	G-A	Homo	INTERGENIC
SBS	Chr11	17563136	T-C	Hetero	INTERGENIC
SBS	Chr11	21610197	T-A	Hetero	NON_SYNONYMOUS_CODING	OsKitaake11g170900
SBS	Chr11	29196733	G-A	Hetero	INTERGENIC
SBS	Chr12	1981510	C-T	Homo	INTERGENIC
SBS	Chr12	9814137	C-T	Hetero	INTERGENIC

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr6	18326	18327	1
Deletion	Chr7	5354544	5354545	1
Deletion	Chr8	5432526	5432528	2
Deletion	Chr5	5510289	5510291	2
Deletion	Chr4	6974092	6974094	2
Deletion	Chr10	8269928	8269930	2
Deletion	Chr1	9648001	9658000	9999	OsKitaake01g123400
Deletion	Chr8	10299652	10299654	2
Deletion	Chr1	13460001	13470000	9999	OsKitaake01g156600
Deletion	Chr10	13789365	13789367	2
Deletion	Chr3	15097267	15097271	4
Deletion	Chr1	17628168	17628170	2
Deletion	Chr10	18690106	18690107	1
Deletion	Chr4	19438001	19447000	8999	OsKitaake04g099601
Deletion	Chr2	22296239	22296241	2
Deletion	Chr3	22837223	22837225	2
Deletion	Chr10	23243098	23243099	1
Deletion	Chr6	25022333	25022341	8
Deletion	Chr6	28875571	28875573	2
Deletion	Chr1	34725538	34725551	13	OsKitaake01g364900
Deletion	Chr3	37587685	37587687	2

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr8	2417562	3315486	2
Inversion	Chr8	18089692	18611758	2
Inversion	Chr1	23039948	23080154	OsKitaake01g219500
Inversion	Chr1	23040016	23080182	OsKitaake01g219500

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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