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Mutant Information

Mutant Name	FN3039-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN3039-S Alignment File
Seed Availability	Yes [Order Seeds]
Phenotype	TO:0000430 (Germination Rate) = Very Low (Below 24%) For more information, please see this phenotype file

Variant Information

Single base substitutions: 33

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 12113672 A-G Hetero INTERGENIC
SBS Chr1 19065213 G-A Hetero INTERGENIC
SBS Chr2 17411821 C-T Hetero INTERGENIC
SBS Chr2 21779698 G-A Hetero INTERGENIC
SBS Chr3 19194386 G-A Hetero INTERGENIC
SBS Chr3 22837251 T-C Hetero INTERGENIC
SBS Chr4 218611 A-G Homo INTERGENIC
SBS Chr4 2464666 T-G Homo INTERGENIC
SBS Chr4 10570125 C-T Homo INTERGENIC
SBS Chr5 141265 A-T Hetero INTERGENIC
SBS Chr5 141269 C-T Hetero INTERGENIC
SBS Chr5 6153711 T-C Hetero INTERGENIC
SBS Chr5 6374383 C-A Hetero INTERGENIC
SBS Chr6 4574591 A-C Hetero INTERGENIC
SBS Chr6 14628202 G-A Hetero INTERGENIC
SBS Chr6 15136596 C-T Hetero INTERGENIC
SBS Chr6 18913281 G-T Homo INTERGENIC
SBS Chr6 21862405 G-C Homo INTERGENIC
SBS Chr7 19406837 A-G Hetero INTERGENIC
SBS Chr8 8643888 A-G Hetero INTERGENIC
SBS Chr8 15991030 G-A Hetero INTERGENIC
SBS Chr8 28765931 G-A Hetero NON_SYNONYMOUS_CODING OsKitaake08g247300
SBS Chr9 1046084 C-T Hetero INTERGENIC
SBS Chr9 1179712 C-T Hetero INTERGENIC
SBS Chr9 3987078 T-A Hetero INTERGENIC
SBS Chr9 9387462 C-T Homo INTERGENIC
SBS Chr9 15573674 A-C Homo INTERGENIC
SBS Chr10 4508849 G-A Hetero INTERGENIC
SBS Chr10 4986664 T-C Hetero INTERGENIC
SBS Chr11 4183409 G-A Homo INTRON
SBS Chr11 18437926 G-A Hetero INTERGENIC
SBS Chr12 7071630 T-A Hetero INTRON
SBS Chr12 26751823 C-T Hetero UTR_3_PRIME

Deletions: 14

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr5 2155954 2155955 1
Deletion Chr5 5220001 5258000 37999 5
Deletion Chr1 8053053 8053086 33
Deletion Chr2 11234348 11234349 1
Deletion Chr2 11582621 11582626 5
Deletion Chr7 12682407 12682411 4
Deletion Chr9 15554838 15554935 97
Deletion Chr4 16745508 16745512 4
Deletion Chr5 17236906 17236907 1
Deletion Chr8 19368470 19368472 2
Deletion Chr6 21344377 21344382 5
Deletion Chr3 25154289 25154291 2
Deletion Chr6 30028001 30034000 5999 2
Deletion Chr2 31380104 31380105 1

Insertions: 6

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr2 7907584 7907587 2
Insertion Chr3 17748028 17748032 3
Insertion Chr4 3416809 3416812 2
Insertion Chr7 21976534 21976537 2
Insertion Chr8 26682322 26682326 3
Insertion Chr12 10853863 10853868 4

Inversions: 4

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Inversion Chr5 5225977 5944592 OsKitaake05g058500
Inversion Chr5 5254891 5944599
Inversion Chr11 25682805 25973996
Inversion Chr11 25682808 25974007

Translocations: 4

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes

Translocation Chr6 12344346 Chr5 116941
Translocation Chr11 18542947 Chr5 24885827 OsKitaake05g217400
Translocation Chr11 18543629 Chr5 24885844 OsKitaake05g217400
Translocation Chr12 24946935 Chr10 7457216

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	12113672	A-G	Hetero	INTERGENIC
SBS	Chr1	19065213	G-A	Hetero	INTERGENIC
SBS	Chr2	17411821	C-T	Hetero	INTERGENIC
SBS	Chr2	21779698	G-A	Hetero	INTERGENIC
SBS	Chr3	19194386	G-A	Hetero	INTERGENIC
SBS	Chr3	22837251	T-C	Hetero	INTERGENIC
SBS	Chr4	218611	A-G	Homo	INTERGENIC
SBS	Chr4	2464666	T-G	Homo	INTERGENIC
SBS	Chr4	10570125	C-T	Homo	INTERGENIC
SBS	Chr5	141265	A-T	Hetero	INTERGENIC
SBS	Chr5	141269	C-T	Hetero	INTERGENIC
SBS	Chr5	6153711	T-C	Hetero	INTERGENIC
SBS	Chr5	6374383	C-A	Hetero	INTERGENIC
SBS	Chr6	4574591	A-C	Hetero	INTERGENIC
SBS	Chr6	14628202	G-A	Hetero	INTERGENIC
SBS	Chr6	15136596	C-T	Hetero	INTERGENIC
SBS	Chr6	18913281	G-T	Homo	INTERGENIC
SBS	Chr6	21862405	G-C	Homo	INTERGENIC
SBS	Chr7	19406837	A-G	Hetero	INTERGENIC
SBS	Chr8	8643888	A-G	Hetero	INTERGENIC
SBS	Chr8	15991030	G-A	Hetero	INTERGENIC
SBS	Chr8	28765931	G-A	Hetero	NON_SYNONYMOUS_CODING	OsKitaake08g247300
SBS	Chr9	1046084	C-T	Hetero	INTERGENIC
SBS	Chr9	1179712	C-T	Hetero	INTERGENIC
SBS	Chr9	3987078	T-A	Hetero	INTERGENIC
SBS	Chr9	9387462	C-T	Homo	INTERGENIC
SBS	Chr9	15573674	A-C	Homo	INTERGENIC
SBS	Chr10	4508849	G-A	Hetero	INTERGENIC
SBS	Chr10	4986664	T-C	Hetero	INTERGENIC
SBS	Chr11	4183409	G-A	Homo	INTRON
SBS	Chr11	18437926	G-A	Hetero	INTERGENIC
SBS	Chr12	7071630	T-A	Hetero	INTRON
SBS	Chr12	26751823	C-T	Hetero	UTR_3_PRIME

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr5	2155954	2155955	1
Deletion	Chr5	5220001	5258000	37999	5
Deletion	Chr1	8053053	8053086	33
Deletion	Chr2	11234348	11234349	1
Deletion	Chr2	11582621	11582626	5
Deletion	Chr7	12682407	12682411	4
Deletion	Chr9	15554838	15554935	97
Deletion	Chr4	16745508	16745512	4
Deletion	Chr5	17236906	17236907	1
Deletion	Chr8	19368470	19368472	2
Deletion	Chr6	21344377	21344382	5
Deletion	Chr3	25154289	25154291	2
Deletion	Chr6	30028001	30034000	5999	2
Deletion	Chr2	31380104	31380105	1

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr5	5225977	5944592	OsKitaake05g058500
Inversion	Chr5	5254891	5944599
Inversion	Chr11	25682805	25973996
Inversion	Chr11	25682808	25974007

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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