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Mutant Information

Mutant Name	FN1297-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN1297-S Alignment File
Seed Availability	Yes [Order Seeds]
Phenotype	TO:0000014 (Panicle Weight) = Low (Between 25% and 74%) TO:0000207 (Plant height) = Normal (Between 75% and 125%) TO:0000445 (Seed Number) = Low (Between 25% and 74%) TO:0000639 (Seed fertility) = Normal (Between 75% and 125%) For more information, please see this phenotype file

Variant Information

Single base substitutions: 53

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 15703059 A-G Hetero INTERGENIC
SBS Chr1 16725165 C-T Hetero INTERGENIC
SBS Chr1 22632439 G-A Hetero UTR_5_PRIME
SBS Chr1 22632440 G-A Hetero UTR_5_PRIME
SBS Chr1 22871621 T-A Hetero INTERGENIC
SBS Chr1 23352540 C-A Hetero NON_SYNONYMOUS_CODING OsKitaake01g223400
SBS Chr1 26633133 A-T Hetero INTERGENIC
SBS Chr1 42376972 G-A Homo INTERGENIC
SBS Chr1 42376975 C-T Homo INTERGENIC
SBS Chr2 9017565 G-C Hetero INTRON
SBS Chr2 18774237 G-A Hetero INTERGENIC
SBS Chr2 20818212 A-T Homo INTRON
SBS Chr3 6512308 G-A Hetero UTR_5_PRIME
SBS Chr3 9990901 T-C Homo INTERGENIC
SBS Chr3 12092959 T-C Hetero INTERGENIC
SBS Chr3 16415326 A-G Homo INTERGENIC
SBS Chr3 18568588 T-C Hetero INTRON
SBS Chr3 20435733 C-T Hetero INTERGENIC
SBS Chr4 4556922 C-T Hetero INTERGENIC
SBS Chr4 12231288 C-T Hetero INTERGENIC
SBS Chr5 30203576 G-A Hetero INTERGENIC
SBS Chr6 314919 A-T Hetero INTERGENIC
SBS Chr6 14262944 G-A Hetero INTERGENIC
SBS Chr6 15347347 A-G Hetero INTERGENIC
SBS Chr6 30630245 T-A Hetero INTERGENIC
SBS Chr7 1136746 A-G Hetero INTERGENIC
SBS Chr7 2050329 C-T Hetero INTERGENIC
SBS Chr7 21963313 G-T Hetero INTERGENIC
SBS Chr7 27774130 T-C Homo NON_SYNONYMOUS_CODING OsKitaake07g259400
SBS Chr8 2241727 T-C Hetero INTERGENIC
SBS Chr8 22850908 G-A Homo INTERGENIC
SBS Chr9 310139 T-G Hetero INTERGENIC
SBS Chr9 5081004 G-A Hetero INTERGENIC
SBS Chr9 6815448 T-A Hetero INTERGENIC
SBS Chr9 11734395 T-C Hetero INTRON
SBS Chr9 12201715 T-C Hetero NON_SYNONYMOUS_CODING OsKitaake09g079100
SBS Chr9 12653480 T-G Hetero INTERGENIC
SBS Chr9 20225056 T-G Homo UTR_5_PRIME
SBS Chr9 20225057 G-T Homo START_GAINED
SBS Chr10 2142505 C-G Hetero INTERGENIC
SBS Chr10 5534804 G-A Hetero INTERGENIC
SBS Chr10 5947082 C-T Hetero INTERGENIC
SBS Chr10 12518753 C-T Hetero UTR_3_PRIME
SBS Chr10 18114047 T-A Hetero INTERGENIC
SBS Chr11 4006105 C-T Homo INTERGENIC
SBS Chr11 19079117 A-G Homo INTERGENIC
SBS Chr11 21519666 A-T Hetero INTERGENIC
SBS Chr12 2793468 A-T Hetero INTERGENIC
SBS Chr12 9611462 G-T Homo INTERGENIC
SBS Chr12 11039182 T-C Homo INTERGENIC
SBS Chr12 17185370 G-A Hetero INTERGENIC
SBS Chr12 21908316 G-A Homo INTERGENIC
SBS Chr12 23791475 C-T Homo INTERGENIC

Deletions: 26

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr1 199577 199579 2
Deletion Chr5 3521144 3521146 2 OsKitaake05g042600
Deletion Chr11 3725100 3725102 2
Deletion Chr10 3872768 3872783 15
Deletion Chr9 4021895 4021897 2
Deletion Chr8 4073615 4073617 2
Deletion Chr12 7334491 7334492 1
Deletion Chr1 8815564 8815575 11
Deletion Chr10 9638949 9638950 1
Deletion Chr7 11075001 11087000 11999 OsKitaake07g104332
Deletion Chr7 11984659 11984660 1
Deletion Chr12 15006507 15006511 4
Deletion Chr3 16337211 16337219 8
Deletion Chr11 18789547 18789548 1
Deletion Chr7 19618001 19682000 63999 6
Deletion Chr5 19884906 19884910 4
Deletion Chr2 20584304 20584305 1
Deletion Chr3 20912768 20912770 2
Deletion Chr1 22629450 22629454 4
Deletion Chr4 23234724 23234728 4
Deletion Chr1 24714001 24739000 24999 2
Deletion Chr1 24766830 24766841 11 OsKitaake01g238900
Deletion Chr4 26494840 26494841 1 OsKitaake04g190200
Deletion Chr5 28202243 28202244 1
Deletion Chr1 32036784 32036790 6
Deletion Chr4 35369562 35369563 1

Insertions: 4

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr3 11619249 11619252 2
Insertion Chr6 8766563 8766566 2
Insertion Chr7 24561726 24561729 2
Insertion Chr10 17165785 17165788 2

Inversions: 2

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Inversion Chr4 10890767 11214936
Inversion Chr4 10890771 11214938

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	15703059	A-G	Hetero	INTERGENIC
SBS	Chr1	16725165	C-T	Hetero	INTERGENIC
SBS	Chr1	22632439	G-A	Hetero	UTR_5_PRIME
SBS	Chr1	22632440	G-A	Hetero	UTR_5_PRIME
SBS	Chr1	22871621	T-A	Hetero	INTERGENIC
SBS	Chr1	23352540	C-A	Hetero	NON_SYNONYMOUS_CODING	OsKitaake01g223400
SBS	Chr1	26633133	A-T	Hetero	INTERGENIC
SBS	Chr1	42376972	G-A	Homo	INTERGENIC
SBS	Chr1	42376975	C-T	Homo	INTERGENIC
SBS	Chr2	9017565	G-C	Hetero	INTRON
SBS	Chr2	18774237	G-A	Hetero	INTERGENIC
SBS	Chr2	20818212	A-T	Homo	INTRON
SBS	Chr3	6512308	G-A	Hetero	UTR_5_PRIME
SBS	Chr3	9990901	T-C	Homo	INTERGENIC
SBS	Chr3	12092959	T-C	Hetero	INTERGENIC
SBS	Chr3	16415326	A-G	Homo	INTERGENIC
SBS	Chr3	18568588	T-C	Hetero	INTRON
SBS	Chr3	20435733	C-T	Hetero	INTERGENIC
SBS	Chr4	4556922	C-T	Hetero	INTERGENIC
SBS	Chr4	12231288	C-T	Hetero	INTERGENIC
SBS	Chr5	30203576	G-A	Hetero	INTERGENIC
SBS	Chr6	314919	A-T	Hetero	INTERGENIC
SBS	Chr6	14262944	G-A	Hetero	INTERGENIC
SBS	Chr6	15347347	A-G	Hetero	INTERGENIC
SBS	Chr6	30630245	T-A	Hetero	INTERGENIC
SBS	Chr7	1136746	A-G	Hetero	INTERGENIC
SBS	Chr7	2050329	C-T	Hetero	INTERGENIC
SBS	Chr7	21963313	G-T	Hetero	INTERGENIC
SBS	Chr7	27774130	T-C	Homo	NON_SYNONYMOUS_CODING	OsKitaake07g259400
SBS	Chr8	2241727	T-C	Hetero	INTERGENIC
SBS	Chr8	22850908	G-A	Homo	INTERGENIC
SBS	Chr9	310139	T-G	Hetero	INTERGENIC
SBS	Chr9	5081004	G-A	Hetero	INTERGENIC
SBS	Chr9	6815448	T-A	Hetero	INTERGENIC
SBS	Chr9	11734395	T-C	Hetero	INTRON
SBS	Chr9	12201715	T-C	Hetero	NON_SYNONYMOUS_CODING	OsKitaake09g079100
SBS	Chr9	12653480	T-G	Hetero	INTERGENIC
SBS	Chr9	20225056	T-G	Homo	UTR_5_PRIME
SBS	Chr9	20225057	G-T	Homo	START_GAINED
SBS	Chr10	2142505	C-G	Hetero	INTERGENIC
SBS	Chr10	5534804	G-A	Hetero	INTERGENIC
SBS	Chr10	5947082	C-T	Hetero	INTERGENIC
SBS	Chr10	12518753	C-T	Hetero	UTR_3_PRIME
SBS	Chr10	18114047	T-A	Hetero	INTERGENIC
SBS	Chr11	4006105	C-T	Homo	INTERGENIC
SBS	Chr11	19079117	A-G	Homo	INTERGENIC
SBS	Chr11	21519666	A-T	Hetero	INTERGENIC
SBS	Chr12	2793468	A-T	Hetero	INTERGENIC
SBS	Chr12	9611462	G-T	Homo	INTERGENIC
SBS	Chr12	11039182	T-C	Homo	INTERGENIC
SBS	Chr12	17185370	G-A	Hetero	INTERGENIC
SBS	Chr12	21908316	G-A	Homo	INTERGENIC
SBS	Chr12	23791475	C-T	Homo	INTERGENIC

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr1	199577	199579	2
Deletion	Chr5	3521144	3521146	2	OsKitaake05g042600
Deletion	Chr11	3725100	3725102	2
Deletion	Chr10	3872768	3872783	15
Deletion	Chr9	4021895	4021897	2
Deletion	Chr8	4073615	4073617	2
Deletion	Chr12	7334491	7334492	1
Deletion	Chr1	8815564	8815575	11
Deletion	Chr10	9638949	9638950	1
Deletion	Chr7	11075001	11087000	11999	OsKitaake07g104332
Deletion	Chr7	11984659	11984660	1
Deletion	Chr12	15006507	15006511	4
Deletion	Chr3	16337211	16337219	8
Deletion	Chr11	18789547	18789548	1
Deletion	Chr7	19618001	19682000	63999	6
Deletion	Chr5	19884906	19884910	4
Deletion	Chr2	20584304	20584305	1
Deletion	Chr3	20912768	20912770	2
Deletion	Chr1	22629450	22629454	4
Deletion	Chr4	23234724	23234728	4
Deletion	Chr1	24714001	24739000	24999	2
Deletion	Chr1	24766830	24766841	11	OsKitaake01g238900
Deletion	Chr4	26494840	26494841	1	OsKitaake04g190200
Deletion	Chr5	28202243	28202244	1
Deletion	Chr1	32036784	32036790	6
Deletion	Chr4	35369562	35369563	1

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr4	10890767	11214936
Inversion	Chr4	10890771	11214938

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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