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Mutant Information

Mutant Name	FN1709-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN1709-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: 33

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 35004482 C-T Homo UTR_3_PRIME
SBS Chr2 6936873 G-A Hetero INTERGENIC
SBS Chr2 10737702 G-A Hetero INTERGENIC
SBS Chr2 19213819 T-C Hetero INTERGENIC
SBS Chr2 20588959 A-G Hetero INTERGENIC
SBS Chr3 4675829 A-G Hetero INTERGENIC
SBS Chr3 16826651 G-A Hetero INTERGENIC
SBS Chr3 22259799 C-T Hetero INTERGENIC
SBS Chr3 26651494 C-T Homo INTERGENIC
SBS Chr3 36827546 C-T Hetero INTERGENIC
SBS Chr3 37605120 G-A Hetero INTRON
SBS Chr4 2655887 A-T Hetero INTERGENIC
SBS Chr4 7831734 C-T Hetero INTERGENIC
SBS Chr4 7927857 G-A Hetero INTERGENIC
SBS Chr4 15384691 C-A Hetero INTERGENIC
SBS Chr4 20710254 G-A Homo NON_SYNONYMOUS_CODING OsKitaake04g112100
SBS Chr4 33263466 C-T Hetero UTR_5_PRIME
SBS Chr5 2047659 C-T Homo INTERGENIC
SBS Chr5 13964120 T-A Hetero INTRON
SBS Chr5 16229502 G-T Hetero INTERGENIC
SBS Chr5 30096571 C-T Homo INTERGENIC
SBS Chr7 11668504 C-T Homo INTERGENIC
SBS Chr7 12242466 A-G Hetero INTERGENIC
SBS Chr7 23642199 G-A Homo INTERGENIC
SBS Chr8 12836223 G-A Hetero INTERGENIC
SBS Chr8 16426641 G-T Hetero INTERGENIC
SBS Chr9 19137679 G-A Hetero INTRON
SBS Chr10 6596861 C-G Homo INTERGENIC
SBS Chr10 12249688 T-A Homo INTERGENIC
SBS Chr10 23595201 G-T Hetero NON_SYNONYMOUS_CODING OsKitaake10g202000
SBS Chr11 14347172 C-T Hetero INTERGENIC
SBS Chr12 9725138 A-G Hetero INTRON
SBS Chr12 15426852 A-G Hetero INTERGENIC

Deletions: 14

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr12 10263001 10307000 43999 2
Deletion Chr12 10310001 10670000 359999 26
Deletion Chr8 10576835 10576837 2
Deletion Chr12 10679001 10872000 192999 11
Deletion Chr12 10883001 10998000 114999 3
Deletion Chr12 11003001 11036000 32999 2
Deletion Chr11 11220777 11220779 2
Deletion Chr7 12748423 12748430 7
Deletion Chr12 16990001 17032000 41999 OsKitaake12g125700
Deletion Chr3 18406781 18406790 9
Deletion Chr4 21575931 21575936 5 OsKitaake04g121800
Deletion Chr5 29461455 29461457 2
Deletion Chr4 31568001 31610000 41999 14
Deletion Chr3 34962717 34962718 1 OsKitaake03g382000

Insertions: 6

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr1 1175746 1175749 2
Insertion Chr10 12871625 12871628 2
Insertion Chr12 1504997 1505000 2
Insertion Chr1 24396360 24396363 2
Insertion Chr2 20550501 20550503 1
Insertion Chr3 32291189 32291191 1

Inversions: 6

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Inversion Chr7 18850107 19092011 OsKitaake07g114200
Inversion Chr7 19092815 19155540 OsKitaake07g155000
Inversion Chr4 21815433 22053103
Inversion Chr4 21815470 22053175
Inversion Chr7 24707783 24777600
Inversion Chr7 24708490 24777602

Translocations: 4

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes

Translocation Chr10 12589767 Chr7 19092011 2
Translocation Chr10 12589772 Chr7 19092714 OsKitaake10g076501
Translocation Chr7 24707787 Chr4 31567749 OsKitaake04g248600
Translocation Chr7 24708489 Chr4 31609851 OsKitaake04g249400

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	35004482	C-T	Homo	UTR_3_PRIME
SBS	Chr2	6936873	G-A	Hetero	INTERGENIC
SBS	Chr2	10737702	G-A	Hetero	INTERGENIC
SBS	Chr2	19213819	T-C	Hetero	INTERGENIC
SBS	Chr2	20588959	A-G	Hetero	INTERGENIC
SBS	Chr3	4675829	A-G	Hetero	INTERGENIC
SBS	Chr3	16826651	G-A	Hetero	INTERGENIC
SBS	Chr3	22259799	C-T	Hetero	INTERGENIC
SBS	Chr3	26651494	C-T	Homo	INTERGENIC
SBS	Chr3	36827546	C-T	Hetero	INTERGENIC
SBS	Chr3	37605120	G-A	Hetero	INTRON
SBS	Chr4	2655887	A-T	Hetero	INTERGENIC
SBS	Chr4	7831734	C-T	Hetero	INTERGENIC
SBS	Chr4	7927857	G-A	Hetero	INTERGENIC
SBS	Chr4	15384691	C-A	Hetero	INTERGENIC
SBS	Chr4	20710254	G-A	Homo	NON_SYNONYMOUS_CODING	OsKitaake04g112100
SBS	Chr4	33263466	C-T	Hetero	UTR_5_PRIME
SBS	Chr5	2047659	C-T	Homo	INTERGENIC
SBS	Chr5	13964120	T-A	Hetero	INTRON
SBS	Chr5	16229502	G-T	Hetero	INTERGENIC
SBS	Chr5	30096571	C-T	Homo	INTERGENIC
SBS	Chr7	11668504	C-T	Homo	INTERGENIC
SBS	Chr7	12242466	A-G	Hetero	INTERGENIC
SBS	Chr7	23642199	G-A	Homo	INTERGENIC
SBS	Chr8	12836223	G-A	Hetero	INTERGENIC
SBS	Chr8	16426641	G-T	Hetero	INTERGENIC
SBS	Chr9	19137679	G-A	Hetero	INTRON
SBS	Chr10	6596861	C-G	Homo	INTERGENIC
SBS	Chr10	12249688	T-A	Homo	INTERGENIC
SBS	Chr10	23595201	G-T	Hetero	NON_SYNONYMOUS_CODING	OsKitaake10g202000
SBS	Chr11	14347172	C-T	Hetero	INTERGENIC
SBS	Chr12	9725138	A-G	Hetero	INTRON
SBS	Chr12	15426852	A-G	Hetero	INTERGENIC

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr12	10263001	10307000	43999	2
Deletion	Chr12	10310001	10670000	359999	26
Deletion	Chr8	10576835	10576837	2
Deletion	Chr12	10679001	10872000	192999	11
Deletion	Chr12	10883001	10998000	114999	3
Deletion	Chr12	11003001	11036000	32999	2
Deletion	Chr11	11220777	11220779	2
Deletion	Chr7	12748423	12748430	7
Deletion	Chr12	16990001	17032000	41999	OsKitaake12g125700
Deletion	Chr3	18406781	18406790	9
Deletion	Chr4	21575931	21575936	5	OsKitaake04g121800
Deletion	Chr5	29461455	29461457	2
Deletion	Chr4	31568001	31610000	41999	14
Deletion	Chr3	34962717	34962718	1	OsKitaake03g382000

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr7	18850107	19092011	OsKitaake07g114200
Inversion	Chr7	19092815	19155540	OsKitaake07g155000
Inversion	Chr4	21815433	22053103
Inversion	Chr4	21815470	22053175
Inversion	Chr7	24707783	24777600
Inversion	Chr7	24708490	24777602

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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