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Mutant Information

Mutant Name	FN498-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN498-S 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: 38

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 35080737 G-A Homo NON_SYNONYMOUS_CODING OsKitaake01g369850
SBS Chr2 20655608 G-A Hetero INTERGENIC
SBS Chr2 35163497 C-A Hetero STOP_GAINED OsKitaake02g368000
SBS Chr3 5309814 A-C Hetero UTR_3_PRIME
SBS Chr3 5722087 A-G Hetero INTRON
SBS Chr3 5876097 G-A Hetero INTERGENIC
SBS Chr3 16955448 C-T Hetero INTRON
SBS Chr3 22540378 C-G Hetero INTERGENIC
SBS Chr3 24224631 G-A Hetero INTERGENIC
SBS Chr3 36961748 C-G Hetero INTERGENIC
SBS Chr4 2151949 G-T Homo INTERGENIC
SBS Chr4 2199048 G-A Homo INTERGENIC
SBS Chr4 16509769 G-T Hetero NON_SYNONYMOUS_CODING OsKitaake04g080300
SBS Chr4 17127295 C-T Homo INTERGENIC
SBS Chr5 1129360 T-A Hetero INTERGENIC
SBS Chr5 1887461 C-A Hetero INTERGENIC
SBS Chr5 1887462 C-A Hetero INTERGENIC
SBS Chr5 5652189 C-T Hetero INTRON
SBS Chr5 7354637 T-A Hetero INTERGENIC
SBS Chr5 12605107 C-T Hetero INTERGENIC
SBS Chr5 21673274 T-C Homo INTERGENIC
SBS Chr6 24545506 A-T Hetero INTRON
SBS Chr8 17654642 T-A Homo INTERGENIC
SBS Chr8 21714854 C-A Hetero NON_SYNONYMOUS_CODING OsKitaake08g164100
SBS Chr8 21731842 A-T Hetero INTERGENIC
SBS Chr8 28413578 G-A Homo INTERGENIC
SBS Chr8 28413579 T-A Homo INTERGENIC
SBS Chr9 6905186 A-G Hetero INTERGENIC
SBS Chr9 10871894 C-T Hetero INTERGENIC
SBS Chr9 11249656 A-G Homo INTERGENIC
SBS Chr9 19723428 C-T Hetero INTERGENIC
SBS Chr9 21414848 A-C Hetero INTERGENIC
SBS Chr10 10829954 C-T Homo INTERGENIC
SBS Chr11 25762337 T-A Homo INTERGENIC
SBS Chr11 27393594 G-A Homo INTERGENIC
SBS Chr12 925844 T-C Homo INTERGENIC
SBS Chr12 13651701 C-T Homo INTERGENIC
SBS Chr12 26964975 C-T Hetero INTERGENIC

Deletions: 19

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr7 4791431 4791439 8
Deletion Chr11 4848801 4848809 8
Deletion Chr7 6183108 6183119 11
Deletion Chr10 8671195 8671360 165
Deletion Chr6 8680868 8680873 5
Deletion Chr3 9331143 9331147 4 OsKitaake03g126800
Deletion Chr5 10674005 10674006 1
Deletion Chr3 12507782 12507791 9
Deletion Chr11 12977184 12977189 5
Deletion Chr5 13842275 13842285 10
Deletion Chr11 18684172 18684174 2
Deletion Chr7 19845704 19845705 1
Deletion Chr4 23262623 23262631 8
Deletion Chr12 24329335 24329340 5
Deletion Chr4 24626754 24626764 10
Deletion Chr12 24916318 24916320 2
Deletion Chr4 28102802 28102803 1
Deletion Chr4 29901334 29901339 5 OsKitaake04g229800
Deletion Chr1 35977030 35977045 15

Insertions: 5

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr3 29711027 29711030 2
Insertion Chr10 6378135 6378140 4
Insertion Chr10 15020081 15020084 2
Insertion Chr11 11862811 11862814 2
Insertion Chr5 4788774 4788776 1

Inversions: 4

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Inversion Chr9 3014355 3021678 OsKitaake09g016000
Inversion Chr9 3014363 3021684 OsKitaake09g016000
Inversion Chr2 10642692 11239306
Inversion Chr2 10642701 11239307

Translocations: 1

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes

Translocation Chr10 12501827 Chr3 7837208 OsKitaake10g075800

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	35080737	G-A	Homo	NON_SYNONYMOUS_CODING	OsKitaake01g369850
SBS	Chr2	20655608	G-A	Hetero	INTERGENIC
SBS	Chr2	35163497	C-A	Hetero	STOP_GAINED	OsKitaake02g368000
SBS	Chr3	5309814	A-C	Hetero	UTR_3_PRIME
SBS	Chr3	5722087	A-G	Hetero	INTRON
SBS	Chr3	5876097	G-A	Hetero	INTERGENIC
SBS	Chr3	16955448	C-T	Hetero	INTRON
SBS	Chr3	22540378	C-G	Hetero	INTERGENIC
SBS	Chr3	24224631	G-A	Hetero	INTERGENIC
SBS	Chr3	36961748	C-G	Hetero	INTERGENIC
SBS	Chr4	2151949	G-T	Homo	INTERGENIC
SBS	Chr4	2199048	G-A	Homo	INTERGENIC
SBS	Chr4	16509769	G-T	Hetero	NON_SYNONYMOUS_CODING	OsKitaake04g080300
SBS	Chr4	17127295	C-T	Homo	INTERGENIC
SBS	Chr5	1129360	T-A	Hetero	INTERGENIC
SBS	Chr5	1887461	C-A	Hetero	INTERGENIC
SBS	Chr5	1887462	C-A	Hetero	INTERGENIC
SBS	Chr5	5652189	C-T	Hetero	INTRON
SBS	Chr5	7354637	T-A	Hetero	INTERGENIC
SBS	Chr5	12605107	C-T	Hetero	INTERGENIC
SBS	Chr5	21673274	T-C	Homo	INTERGENIC
SBS	Chr6	24545506	A-T	Hetero	INTRON
SBS	Chr8	17654642	T-A	Homo	INTERGENIC
SBS	Chr8	21714854	C-A	Hetero	NON_SYNONYMOUS_CODING	OsKitaake08g164100
SBS	Chr8	21731842	A-T	Hetero	INTERGENIC
SBS	Chr8	28413578	G-A	Homo	INTERGENIC
SBS	Chr8	28413579	T-A	Homo	INTERGENIC
SBS	Chr9	6905186	A-G	Hetero	INTERGENIC
SBS	Chr9	10871894	C-T	Hetero	INTERGENIC
SBS	Chr9	11249656	A-G	Homo	INTERGENIC
SBS	Chr9	19723428	C-T	Hetero	INTERGENIC
SBS	Chr9	21414848	A-C	Hetero	INTERGENIC
SBS	Chr10	10829954	C-T	Homo	INTERGENIC
SBS	Chr11	25762337	T-A	Homo	INTERGENIC
SBS	Chr11	27393594	G-A	Homo	INTERGENIC
SBS	Chr12	925844	T-C	Homo	INTERGENIC
SBS	Chr12	13651701	C-T	Homo	INTERGENIC
SBS	Chr12	26964975	C-T	Hetero	INTERGENIC

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr7	4791431	4791439	8
Deletion	Chr11	4848801	4848809	8
Deletion	Chr7	6183108	6183119	11
Deletion	Chr10	8671195	8671360	165
Deletion	Chr6	8680868	8680873	5
Deletion	Chr3	9331143	9331147	4	OsKitaake03g126800
Deletion	Chr5	10674005	10674006	1
Deletion	Chr3	12507782	12507791	9
Deletion	Chr11	12977184	12977189	5
Deletion	Chr5	13842275	13842285	10
Deletion	Chr11	18684172	18684174	2
Deletion	Chr7	19845704	19845705	1
Deletion	Chr4	23262623	23262631	8
Deletion	Chr12	24329335	24329340	5
Deletion	Chr4	24626754	24626764	10
Deletion	Chr12	24916318	24916320	2
Deletion	Chr4	28102802	28102803	1
Deletion	Chr4	29901334	29901339	5	OsKitaake04g229800
Deletion	Chr1	35977030	35977045	15

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr9	3014355	3021678	OsKitaake09g016000
Inversion	Chr9	3014363	3021684	OsKitaake09g016000
Inversion	Chr2	10642692	11239306
Inversion	Chr2	10642701	11239307

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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