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Mutant Information

SOS indicates the sequenced line is sterile and seeds from siblings are available.

Mutant Name	FN-289 [Download]
Generation	M2-SOS
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN-289 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) = Normal (Between 75% and 125%) TO:0000639 (Seed fertility) = Low (Between 25% and 74%) For more information, please see this phenotype file

Variant Information

Single base substitutions: 28

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 16822096 A-G Homo INTERGENIC
SBS Chr1 38056140 G-T Homo INTERGENIC
SBS Chr1 38056143 G-A Homo INTERGENIC
SBS Chr1 38056144 G-A Homo INTERGENIC
SBS Chr2 2121679 C-T Hetero INTERGENIC
SBS Chr2 3658164 C-G Hetero INTERGENIC
SBS Chr2 7897040 G-A Hetero INTERGENIC
SBS Chr2 18884367 A-G Hetero INTERGENIC
SBS Chr2 32571740 T-G Homo INTERGENIC
SBS Chr3 3392938 C-T Hetero INTERGENIC
SBS Chr4 36583219 C-T Homo INTERGENIC
SBS Chr6 19257434 C-T Homo INTERGENIC
SBS Chr7 4083480 T-G Hetero INTERGENIC
SBS Chr7 12974690 T-A Hetero INTRON
SBS Chr7 17116906 C-G Hetero INTERGENIC
SBS Chr7 23048917 C-T Hetero NON_SYNONYMOUS_CODING OsKitaake07g198500
SBS Chr7 26186942 C-G Homo NON_SYNONYMOUS_CODING OsKitaake07g240200
SBS Chr8 24238292 T-A Hetero INTERGENIC
SBS Chr9 4114781 T-A Homo INTERGENIC
SBS Chr9 13435738 C-T Homo INTERGENIC
SBS Chr11 9272937 T-C Homo INTERGENIC
SBS Chr11 15732568 T-A Homo NON_SYNONYMOUS_CODING OsKitaake11g126400
SBS Chr11 28018991 G-A Hetero INTERGENIC
SBS Chr12 652737 G-A Homo INTERGENIC
SBS Chr12 5090390 T-A Hetero INTRON
SBS Chr12 6570685 G-A Hetero INTERGENIC
SBS Chr12 18545389 A-G Homo NON_SYNONYMOUS_CODING OsKitaake12g135500
SBS Chr12 24497539 A-C Homo NON_SYNONYMOUS_CODING OsKitaake12g197600

Deletions: 12

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr9 9460840 9460841 1
Deletion Chr1 13848306 13848308 2
Deletion Chr8 17945391 17945395 4
Deletion Chr8 18704697 18704699 2
Deletion Chr1 19919089 19919094 5
Deletion Chr6 20462757 20462758 1
Deletion Chr1 25831797 25831809 12
Deletion Chr3 28628833 28628834 1
Deletion Chr8 28695430 28695443 13 OsKitaake08g246100
Deletion Chr5 29003376 29003397 21
Deletion Chr1 29427584 29427585 1
Deletion Chr1 39862188 39862298 110

Insertions: 2

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr3 25610951 25610954 2
Insertion Chr9 20279053 20279056 2

Inversions: 3

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Inversion Chr8 14087443 14175857
Inversion Chr8 14087674 14175878
Inversion Chr6 14422594 14749027

Translocations: 5

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes

Translocation Chr8 14087456 Chr4 25343099 OsKitaake04g172800
Translocation Chr8 14087672 Chr4 25343103 OsKitaake04g172800
Translocation Chr10 15777320 Chr6 6447163
Translocation Chr12 23195639 Chr5 11040645 2
Translocation Chr12 23196125 Chr5 11040642 2

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	16822096	A-G	Homo	INTERGENIC
SBS	Chr1	38056140	G-T	Homo	INTERGENIC
SBS	Chr1	38056143	G-A	Homo	INTERGENIC
SBS	Chr1	38056144	G-A	Homo	INTERGENIC
SBS	Chr2	2121679	C-T	Hetero	INTERGENIC
SBS	Chr2	3658164	C-G	Hetero	INTERGENIC
SBS	Chr2	7897040	G-A	Hetero	INTERGENIC
SBS	Chr2	18884367	A-G	Hetero	INTERGENIC
SBS	Chr2	32571740	T-G	Homo	INTERGENIC
SBS	Chr3	3392938	C-T	Hetero	INTERGENIC
SBS	Chr4	36583219	C-T	Homo	INTERGENIC
SBS	Chr6	19257434	C-T	Homo	INTERGENIC
SBS	Chr7	4083480	T-G	Hetero	INTERGENIC
SBS	Chr7	12974690	T-A	Hetero	INTRON
SBS	Chr7	17116906	C-G	Hetero	INTERGENIC
SBS	Chr7	23048917	C-T	Hetero	NON_SYNONYMOUS_CODING	OsKitaake07g198500
SBS	Chr7	26186942	C-G	Homo	NON_SYNONYMOUS_CODING	OsKitaake07g240200
SBS	Chr8	24238292	T-A	Hetero	INTERGENIC
SBS	Chr9	4114781	T-A	Homo	INTERGENIC
SBS	Chr9	13435738	C-T	Homo	INTERGENIC
SBS	Chr11	9272937	T-C	Homo	INTERGENIC
SBS	Chr11	15732568	T-A	Homo	NON_SYNONYMOUS_CODING	OsKitaake11g126400
SBS	Chr11	28018991	G-A	Hetero	INTERGENIC
SBS	Chr12	652737	G-A	Homo	INTERGENIC
SBS	Chr12	5090390	T-A	Hetero	INTRON
SBS	Chr12	6570685	G-A	Hetero	INTERGENIC
SBS	Chr12	18545389	A-G	Homo	NON_SYNONYMOUS_CODING	OsKitaake12g135500
SBS	Chr12	24497539	A-C	Homo	NON_SYNONYMOUS_CODING	OsKitaake12g197600

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr9	9460840	9460841	1
Deletion	Chr1	13848306	13848308	2
Deletion	Chr8	17945391	17945395	4
Deletion	Chr8	18704697	18704699	2
Deletion	Chr1	19919089	19919094	5
Deletion	Chr6	20462757	20462758	1
Deletion	Chr1	25831797	25831809	12
Deletion	Chr3	28628833	28628834	1
Deletion	Chr8	28695430	28695443	13	OsKitaake08g246100
Deletion	Chr5	29003376	29003397	21
Deletion	Chr1	29427584	29427585	1
Deletion	Chr1	39862188	39862298	110

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr8	14087443	14175857
Inversion	Chr8	14087674	14175878
Inversion	Chr6	14422594	14749027

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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