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Mutant Information

Mutant Name	FN1499-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN1499-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: 41

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 7021732 C-T Hetero INTERGENIC
SBS Chr1 7873921 G-T Hetero INTERGENIC
SBS Chr1 23099018 C-T Hetero INTRON
SBS Chr2 2344476 A-G Hetero INTERGENIC
SBS Chr2 8509258 G-A Hetero INTERGENIC
SBS Chr2 9362688 G-A Homo INTERGENIC
SBS Chr2 30583568 T-C Hetero UTR_5_PRIME
SBS Chr2 32575450 T-C Hetero INTERGENIC
SBS Chr2 33644532 T-C Hetero INTERGENIC
SBS Chr2 35211551 C-G Homo INTRON
SBS Chr3 15167380 C-T Hetero INTERGENIC
SBS Chr3 27494682 A-T Homo INTERGENIC
SBS Chr4 799643 C-T Hetero INTERGENIC
SBS Chr4 4038058 C-T Homo INTERGENIC
SBS Chr4 21809459 C-T Hetero INTERGENIC
SBS Chr5 2000146 A-T Homo INTERGENIC
SBS Chr5 2228587 G-A Homo UTR_3_PRIME
SBS Chr5 20033293 A-T Homo INTERGENIC
SBS Chr6 8268514 G-A Hetero INTERGENIC
SBS Chr6 22438074 C-T Hetero INTERGENIC
SBS Chr7 595414 A-C Hetero INTRON
SBS Chr7 3915574 G-A Hetero INTERGENIC
SBS Chr7 8632162 G-A Hetero INTERGENIC
SBS Chr8 15259643 A-T Hetero INTERGENIC
SBS Chr8 18878122 A-T Homo INTERGENIC
SBS Chr9 14915184 A-G Hetero INTERGENIC
SBS Chr9 20362020 A-T Hetero INTERGENIC
SBS Chr10 1368527 C-T Hetero INTERGENIC
SBS Chr10 4597892 C-T Hetero INTERGENIC
SBS Chr10 4742750 A-G Hetero INTERGENIC
SBS Chr10 7748482 C-A Homo INTERGENIC
SBS Chr10 10504836 C-T Homo NON_SYNONYMOUS_CODING OsKitaake10g061500
SBS Chr10 11608105 A-T Homo INTERGENIC
SBS Chr10 13090580 G-T Homo INTERGENIC
SBS Chr11 1627556 T-A Hetero INTRON
SBS Chr11 15533682 G-A Hetero INTERGENIC
SBS Chr11 28846833 C-A Hetero NON_SYNONYMOUS_CODING OsKitaake11g236100
SBS Chr12 4642714 A-G Hetero INTERGENIC
SBS Chr12 14417809 G-A Hetero INTRON
SBS Chr12 16025334 A-G Hetero INTRON
SBS Chr12 22073088 G-A Hetero INTERGENIC

Deletions: 9

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr5 470001 500000 29999 OsKitaake05g005866
Deletion Chr1 1339465 1339467 2
Deletion Chr1 3850662 3850664 2
Deletion Chr8 5076763 5076764 1
Deletion Chr4 6919001 6931000 11999
Deletion Chr1 9606641 9606643 2
Deletion Chr12 9876659 9876805 146
Deletion Chr8 18610429 18610439 10
Deletion Chr5 20971582 20971585 3

Insertions: 2

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr2 29292738 29292741 2 OsKitaake02g294500
Insertion Chr12 11661870 11661872 1

Inversions: 6

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Inversion Chr10 1367281 1769481 OsKitaake10g012900
Inversion Chr10 1367296 1769496 OsKitaake10g012900
Inversion Chr12 16074114 16558816
Inversion Chr12 16074172 16558816
Inversion Chr4 33021557 33713658 OsKitaake04g280100
Inversion Chr4 33147607 33317244 2

Translocations: 2

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes

Translocation Chr10 12105212 Chr4 33146505
Translocation Chr10 12110531 Chr4 33147499 OsKitaake04g269800

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	7021732	C-T	Hetero	INTERGENIC
SBS	Chr1	7873921	G-T	Hetero	INTERGENIC
SBS	Chr1	23099018	C-T	Hetero	INTRON
SBS	Chr2	2344476	A-G	Hetero	INTERGENIC
SBS	Chr2	8509258	G-A	Hetero	INTERGENIC
SBS	Chr2	9362688	G-A	Homo	INTERGENIC
SBS	Chr2	30583568	T-C	Hetero	UTR_5_PRIME
SBS	Chr2	32575450	T-C	Hetero	INTERGENIC
SBS	Chr2	33644532	T-C	Hetero	INTERGENIC
SBS	Chr2	35211551	C-G	Homo	INTRON
SBS	Chr3	15167380	C-T	Hetero	INTERGENIC
SBS	Chr3	27494682	A-T	Homo	INTERGENIC
SBS	Chr4	799643	C-T	Hetero	INTERGENIC
SBS	Chr4	4038058	C-T	Homo	INTERGENIC
SBS	Chr4	21809459	C-T	Hetero	INTERGENIC
SBS	Chr5	2000146	A-T	Homo	INTERGENIC
SBS	Chr5	2228587	G-A	Homo	UTR_3_PRIME
SBS	Chr5	20033293	A-T	Homo	INTERGENIC
SBS	Chr6	8268514	G-A	Hetero	INTERGENIC
SBS	Chr6	22438074	C-T	Hetero	INTERGENIC
SBS	Chr7	595414	A-C	Hetero	INTRON
SBS	Chr7	3915574	G-A	Hetero	INTERGENIC
SBS	Chr7	8632162	G-A	Hetero	INTERGENIC
SBS	Chr8	15259643	A-T	Hetero	INTERGENIC
SBS	Chr8	18878122	A-T	Homo	INTERGENIC
SBS	Chr9	14915184	A-G	Hetero	INTERGENIC
SBS	Chr9	20362020	A-T	Hetero	INTERGENIC
SBS	Chr10	1368527	C-T	Hetero	INTERGENIC
SBS	Chr10	4597892	C-T	Hetero	INTERGENIC
SBS	Chr10	4742750	A-G	Hetero	INTERGENIC
SBS	Chr10	7748482	C-A	Homo	INTERGENIC
SBS	Chr10	10504836	C-T	Homo	NON_SYNONYMOUS_CODING	OsKitaake10g061500
SBS	Chr10	11608105	A-T	Homo	INTERGENIC
SBS	Chr10	13090580	G-T	Homo	INTERGENIC
SBS	Chr11	1627556	T-A	Hetero	INTRON
SBS	Chr11	15533682	G-A	Hetero	INTERGENIC
SBS	Chr11	28846833	C-A	Hetero	NON_SYNONYMOUS_CODING	OsKitaake11g236100
SBS	Chr12	4642714	A-G	Hetero	INTERGENIC
SBS	Chr12	14417809	G-A	Hetero	INTRON
SBS	Chr12	16025334	A-G	Hetero	INTRON
SBS	Chr12	22073088	G-A	Hetero	INTERGENIC

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr5	470001	500000	29999	OsKitaake05g005866
Deletion	Chr1	1339465	1339467	2
Deletion	Chr1	3850662	3850664	2
Deletion	Chr8	5076763	5076764	1
Deletion	Chr4	6919001	6931000	11999
Deletion	Chr1	9606641	9606643	2
Deletion	Chr12	9876659	9876805	146
Deletion	Chr8	18610429	18610439	10
Deletion	Chr5	20971582	20971585	3

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr10	1367281	1769481	OsKitaake10g012900
Inversion	Chr10	1367296	1769496	OsKitaake10g012900
Inversion	Chr12	16074114	16558816
Inversion	Chr12	16074172	16558816
Inversion	Chr4	33021557	33713658	OsKitaake04g280100
Inversion	Chr4	33147607	33317244	2

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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