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Mutant Information

Mutant Name	FN1540-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN1540-S Alignment File
Seed Availability	Yes [Order Seeds]
Phenotype	TO:0000326 (Leaf Color) = Normal 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: 43

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 8277548 T-G Hetero INTERGENIC
SBS Chr1 17235667 C-T Homo INTERGENIC
SBS Chr1 38113432 A-G Hetero INTERGENIC
SBS Chr1 42183125 G-T Homo INTERGENIC
SBS Chr2 29869732 T-C Homo INTRON
SBS Chr2 30192311 G-T Hetero INTRON
SBS Chr3 13660205 T-A Homo INTERGENIC
SBS Chr3 25200062 C-A Hetero INTERGENIC
SBS Chr4 272397 T-G Homo INTERGENIC
SBS Chr4 1298413 A-G Homo INTERGENIC
SBS Chr4 21816305 C-T Hetero INTERGENIC
SBS Chr4 28555057 T-A Hetero INTRON
SBS Chr4 29594537 C-A Hetero INTRON
SBS Chr5 1580827 A-G Hetero INTERGENIC
SBS Chr5 12837551 A-T Homo INTERGENIC
SBS Chr5 15272884 C-T Hetero INTERGENIC
SBS Chr5 24739171 G-A Hetero INTERGENIC
SBS Chr5 27264805 A-G Hetero INTERGENIC
SBS Chr6 3844910 G-A Hetero INTERGENIC
SBS Chr6 3844911 C-A Hetero INTERGENIC
SBS Chr6 25662762 G-A Hetero INTERGENIC
SBS Chr7 23852675 T-G Hetero INTERGENIC
SBS Chr7 23928772 T-C Hetero INTERGENIC
SBS Chr8 13359812 T-C Hetero INTERGENIC
SBS Chr8 13376551 C-A Hetero INTRON
SBS Chr8 13376552 C-A Hetero INTRON
SBS Chr8 14690712 A-C Hetero INTERGENIC
SBS Chr8 20168234 A-G Hetero INTERGENIC
SBS Chr8 23142619 A-G Hetero INTERGENIC
SBS Chr9 2870113 C-A Hetero INTERGENIC
SBS Chr9 5198894 T-A Hetero INTERGENIC
SBS Chr9 22365320 G-C Homo NON_SYNONYMOUS_CODING OsKitaake09g202900
SBS Chr11 9665332 G-T Hetero INTERGENIC
SBS Chr11 12922601 T-A Hetero INTERGENIC
SBS Chr11 15133931 G-A Homo INTERGENIC
SBS Chr11 21432594 A-G Homo INTERGENIC
SBS Chr11 21812331 T-C Hetero INTERGENIC
SBS Chr11 27411832 G-A Hetero INTERGENIC
SBS Chr11 28191419 G-T Hetero NON_SYNONYMOUS_CODING OsKitaake11g231500
SBS Chr12 10332394 C-A Hetero INTERGENIC
SBS Chr12 10696832 A-T Hetero INTERGENIC
SBS Chr12 21366891 G-A Hetero INTERGENIC
SBS Chr12 25009066 G-C Hetero INTERGENIC

Deletions: 18

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr6 88291 88645 354
Deletion Chr8 2936001 2965000 28999 2
Deletion Chr2 3847863 3847878 15
Deletion Chr11 3971987 3971989 2
Deletion Chr1 5448310 5448314 4
Deletion Chr5 5594725 5594731 6
Deletion Chr4 5728972 5728973 1
Deletion Chr2 9304360 9304371 11
Deletion Chr4 10800644 10800650 6
Deletion Chr6 18260956 18260958 2
Deletion Chr11 18871125 18871126 1
Deletion Chr6 20929557 20929559 2
Deletion Chr8 22711430 22711443 13
Deletion Chr4 24778681 24778682 1
Deletion Chr8 25383233 25383241 8
Deletion Chr2 26280844 26280845 1
Deletion Chr3 28579750 28579752 2
Deletion Chr4 33660528 33660529 1

Insertions: 3

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr1 12543425 12543428 2
Insertion Chr5 11018528 11018531 2
Insertion Chr10 5735714 5735716 1

Inversions: 4

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Inversion Chr3 3079620 3285575
Inversion Chr3 3285584 3384515
Inversion Chr8 12599489 13263955 OsKitaake08g107900
Inversion Chr8 12600792 13263984 OsKitaake08g107900

Translocations: 4

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes

Translocation Chr3 3079625 Chr2 26911282
Translocation Chr3 3384507 Chr2 26911971
Translocation Chr11 14550974 Chr8 12600777 2
Translocation Chr11 14550975 Chr8 12599488 2

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	8277548	T-G	Hetero	INTERGENIC
SBS	Chr1	17235667	C-T	Homo	INTERGENIC
SBS	Chr1	38113432	A-G	Hetero	INTERGENIC
SBS	Chr1	42183125	G-T	Homo	INTERGENIC
SBS	Chr2	29869732	T-C	Homo	INTRON
SBS	Chr2	30192311	G-T	Hetero	INTRON
SBS	Chr3	13660205	T-A	Homo	INTERGENIC
SBS	Chr3	25200062	C-A	Hetero	INTERGENIC
SBS	Chr4	272397	T-G	Homo	INTERGENIC
SBS	Chr4	1298413	A-G	Homo	INTERGENIC
SBS	Chr4	21816305	C-T	Hetero	INTERGENIC
SBS	Chr4	28555057	T-A	Hetero	INTRON
SBS	Chr4	29594537	C-A	Hetero	INTRON
SBS	Chr5	1580827	A-G	Hetero	INTERGENIC
SBS	Chr5	12837551	A-T	Homo	INTERGENIC
SBS	Chr5	15272884	C-T	Hetero	INTERGENIC
SBS	Chr5	24739171	G-A	Hetero	INTERGENIC
SBS	Chr5	27264805	A-G	Hetero	INTERGENIC
SBS	Chr6	3844910	G-A	Hetero	INTERGENIC
SBS	Chr6	3844911	C-A	Hetero	INTERGENIC
SBS	Chr6	25662762	G-A	Hetero	INTERGENIC
SBS	Chr7	23852675	T-G	Hetero	INTERGENIC
SBS	Chr7	23928772	T-C	Hetero	INTERGENIC
SBS	Chr8	13359812	T-C	Hetero	INTERGENIC
SBS	Chr8	13376551	C-A	Hetero	INTRON
SBS	Chr8	13376552	C-A	Hetero	INTRON
SBS	Chr8	14690712	A-C	Hetero	INTERGENIC
SBS	Chr8	20168234	A-G	Hetero	INTERGENIC
SBS	Chr8	23142619	A-G	Hetero	INTERGENIC
SBS	Chr9	2870113	C-A	Hetero	INTERGENIC
SBS	Chr9	5198894	T-A	Hetero	INTERGENIC
SBS	Chr9	22365320	G-C	Homo	NON_SYNONYMOUS_CODING	OsKitaake09g202900
SBS	Chr11	9665332	G-T	Hetero	INTERGENIC
SBS	Chr11	12922601	T-A	Hetero	INTERGENIC
SBS	Chr11	15133931	G-A	Homo	INTERGENIC
SBS	Chr11	21432594	A-G	Homo	INTERGENIC
SBS	Chr11	21812331	T-C	Hetero	INTERGENIC
SBS	Chr11	27411832	G-A	Hetero	INTERGENIC
SBS	Chr11	28191419	G-T	Hetero	NON_SYNONYMOUS_CODING	OsKitaake11g231500
SBS	Chr12	10332394	C-A	Hetero	INTERGENIC
SBS	Chr12	10696832	A-T	Hetero	INTERGENIC
SBS	Chr12	21366891	G-A	Hetero	INTERGENIC
SBS	Chr12	25009066	G-C	Hetero	INTERGENIC

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr6	88291	88645	354
Deletion	Chr8	2936001	2965000	28999	2
Deletion	Chr2	3847863	3847878	15
Deletion	Chr11	3971987	3971989	2
Deletion	Chr1	5448310	5448314	4
Deletion	Chr5	5594725	5594731	6
Deletion	Chr4	5728972	5728973	1
Deletion	Chr2	9304360	9304371	11
Deletion	Chr4	10800644	10800650	6
Deletion	Chr6	18260956	18260958	2
Deletion	Chr11	18871125	18871126	1
Deletion	Chr6	20929557	20929559	2
Deletion	Chr8	22711430	22711443	13
Deletion	Chr4	24778681	24778682	1
Deletion	Chr8	25383233	25383241	8
Deletion	Chr2	26280844	26280845	1
Deletion	Chr3	28579750	28579752	2
Deletion	Chr4	33660528	33660529	1

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr3	3079620	3285575
Inversion	Chr3	3285584	3384515
Inversion	Chr8	12599489	13263955	OsKitaake08g107900
Inversion	Chr8	12600792	13263984	OsKitaake08g107900

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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