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Mutant Information

Mutant Name	FN1529-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN1529-S Alignment File
Seed Availability	Yes [Order Seeds]
Phenotype	TO:0000326 (Leaf Color) = Normal TO:0000346 (Tiller number) = Low (Between 25% and 74%) TO:0000430 (Germination Rate) = Low (Between 25% and 75%) For more information, please see this phenotype file

Variant Information

Single base substitutions: 56

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 2026204 T-C Hetero INTERGENIC
SBS Chr1 4059526 C-G Hetero INTERGENIC
SBS Chr1 7768729 C-T Homo INTERGENIC
SBS Chr1 21616904 C-A Homo INTERGENIC
SBS Chr1 29279909 C-T Hetero INTERGENIC
SBS Chr2 14673136 C-T Hetero INTERGENIC
SBS Chr2 18253975 A-G Hetero INTERGENIC
SBS Chr2 18534951 C-A Hetero INTERGENIC
SBS Chr2 24652320 A-T Homo NON_SYNONYMOUS_CODING OsKitaake02g245100
SBS Chr2 31239757 T-C Homo INTERGENIC
SBS Chr3 14871104 G-A Hetero INTERGENIC
SBS Chr3 20234929 C-T Homo INTERGENIC
SBS Chr3 21471836 C-T Hetero INTERGENIC
SBS Chr3 23511412 C-A Homo INTERGENIC
SBS Chr3 34425196 C-T Homo INTERGENIC
SBS Chr4 440343 G-A Hetero INTERGENIC
SBS Chr4 8755355 C-T Homo UTR_3_PRIME
SBS Chr4 8755356 A-T Homo UTR_3_PRIME
SBS Chr4 8755357 A-T Homo UTR_3_PRIME
SBS Chr4 28087754 A-G Homo INTERGENIC
SBS Chr5 20169101 A-G Homo INTERGENIC
SBS Chr5 29073956 T-G Homo INTRON
SBS Chr5 29699714 C-T Homo INTERGENIC
SBS Chr6 27293258 G-A Homo INTERGENIC
SBS Chr6 28066999 A-T Hetero INTERGENIC
SBS Chr7 6032644 C-T Hetero INTERGENIC
SBS Chr7 6417437 A-G Hetero INTERGENIC
SBS Chr7 11970870 G-A Hetero INTERGENIC
SBS Chr7 21629811 G-C Hetero INTERGENIC
SBS Chr7 29606241 T-C Hetero SPLICE_SITE_REGION
SBS Chr8 1040224 A-C Hetero INTERGENIC
SBS Chr8 3835949 G-A Hetero INTERGENIC
SBS Chr8 15817924 A-G Hetero INTERGENIC
SBS Chr8 16064093 C-A Hetero INTERGENIC
SBS Chr8 18877330 T-C Hetero INTERGENIC
SBS Chr8 21552717 A-C Homo INTERGENIC
SBS Chr8 28463363 A-G Hetero INTERGENIC
SBS Chr9 1460522 T-G Hetero INTERGENIC
SBS Chr9 22742243 G-C Homo INTRON
SBS Chr10 7707566 G-C Hetero INTERGENIC
SBS Chr10 11720593 T-C Hetero INTERGENIC
SBS Chr10 13804402 A-C Hetero INTERGENIC
SBS Chr11 1406215 T-C Hetero INTRON
SBS Chr11 2228558 T-C Hetero INTRON
SBS Chr11 2630935 C-T Hetero INTERGENIC
SBS Chr11 7076595 A-T Hetero INTERGENIC
SBS Chr11 7497439 C-T Hetero INTERGENIC
SBS Chr11 7624368 G-T Hetero INTERGENIC
SBS Chr11 12020299 T-C Hetero INTRON
SBS Chr11 24376667 G-A Hetero INTERGENIC
SBS Chr11 27298642 G-A Hetero INTERGENIC
SBS Chr12 4910705 C-T Hetero INTERGENIC
SBS Chr12 5171150 G-C Homo INTRON
SBS Chr12 8336987 C-T Homo INTRON
SBS Chr12 15166941 C-G Hetero INTERGENIC
SBS Chr12 21519852 A-C Hetero INTERGENIC

Deletions: 22

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr10 1573313 1573314 1
Deletion Chr6 2623780 2623785 5
Deletion Chr11 5687568 5687573 5
Deletion Chr4 11159001 11187000 27999
Deletion Chr7 11272458 11272461 3
Deletion Chr11 11795885 11795887 2
Deletion Chr2 15133001 15143000 9999
Deletion Chr10 16009693 16009695 2
Deletion Chr2 19002650 19002652 2 OsKitaake02g186101
Deletion Chr2 19196001 19279000 82999 8
Deletion Chr3 19222860 19222864 4
Deletion Chr2 19363001 19416000 52999 5
Deletion Chr7 20057315 20057319 4
Deletion Chr2 23637975 23637980 5
Deletion Chr1 25378982 25378988 6
Deletion Chr1 26171001 26347000 175999 16
Deletion Chr2 27499311 27499316 5
Deletion Chr2 29598877 29598889 12
Deletion Chr2 29763889 29763890 1
Deletion Chr1 33153903 33153905 2 OsKitaake01g338400
Deletion Chr4 34779212 34779220 8
Deletion Chr1 41760844 41760852 8

Insertions: 3

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr3 35298583 35298586 2
Insertion Chr6 7536891 7536893 1
Insertion Chr12 19586979 19586982 2

Inversions: 1

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Inversion Chr2 19274903 19288388

Translocations: 5

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes

Translocation Chr11 6896294 Chr3 18919993
Translocation Chr10 14294541 Chr3 18918863 OsKitaake10g089400
Translocation Chr11 18587347 Chr10 14294075 OsKitaake11g144000
Translocation Chr2 21544504 Chr1 26345521 OsKitaake02g208400
Translocation Chr2 21544515 Chr1 26346550 OsKitaake02g208400

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	2026204	T-C	Hetero	INTERGENIC
SBS	Chr1	4059526	C-G	Hetero	INTERGENIC
SBS	Chr1	7768729	C-T	Homo	INTERGENIC
SBS	Chr1	21616904	C-A	Homo	INTERGENIC
SBS	Chr1	29279909	C-T	Hetero	INTERGENIC
SBS	Chr2	14673136	C-T	Hetero	INTERGENIC
SBS	Chr2	18253975	A-G	Hetero	INTERGENIC
SBS	Chr2	18534951	C-A	Hetero	INTERGENIC
SBS	Chr2	24652320	A-T	Homo	NON_SYNONYMOUS_CODING	OsKitaake02g245100
SBS	Chr2	31239757	T-C	Homo	INTERGENIC
SBS	Chr3	14871104	G-A	Hetero	INTERGENIC
SBS	Chr3	20234929	C-T	Homo	INTERGENIC
SBS	Chr3	21471836	C-T	Hetero	INTERGENIC
SBS	Chr3	23511412	C-A	Homo	INTERGENIC
SBS	Chr3	34425196	C-T	Homo	INTERGENIC
SBS	Chr4	440343	G-A	Hetero	INTERGENIC
SBS	Chr4	8755355	C-T	Homo	UTR_3_PRIME
SBS	Chr4	8755356	A-T	Homo	UTR_3_PRIME
SBS	Chr4	8755357	A-T	Homo	UTR_3_PRIME
SBS	Chr4	28087754	A-G	Homo	INTERGENIC
SBS	Chr5	20169101	A-G	Homo	INTERGENIC
SBS	Chr5	29073956	T-G	Homo	INTRON
SBS	Chr5	29699714	C-T	Homo	INTERGENIC
SBS	Chr6	27293258	G-A	Homo	INTERGENIC
SBS	Chr6	28066999	A-T	Hetero	INTERGENIC
SBS	Chr7	6032644	C-T	Hetero	INTERGENIC
SBS	Chr7	6417437	A-G	Hetero	INTERGENIC
SBS	Chr7	11970870	G-A	Hetero	INTERGENIC
SBS	Chr7	21629811	G-C	Hetero	INTERGENIC
SBS	Chr7	29606241	T-C	Hetero	SPLICE_SITE_REGION
SBS	Chr8	1040224	A-C	Hetero	INTERGENIC
SBS	Chr8	3835949	G-A	Hetero	INTERGENIC
SBS	Chr8	15817924	A-G	Hetero	INTERGENIC
SBS	Chr8	16064093	C-A	Hetero	INTERGENIC
SBS	Chr8	18877330	T-C	Hetero	INTERGENIC
SBS	Chr8	21552717	A-C	Homo	INTERGENIC
SBS	Chr8	28463363	A-G	Hetero	INTERGENIC
SBS	Chr9	1460522	T-G	Hetero	INTERGENIC
SBS	Chr9	22742243	G-C	Homo	INTRON
SBS	Chr10	7707566	G-C	Hetero	INTERGENIC
SBS	Chr10	11720593	T-C	Hetero	INTERGENIC
SBS	Chr10	13804402	A-C	Hetero	INTERGENIC
SBS	Chr11	1406215	T-C	Hetero	INTRON
SBS	Chr11	2228558	T-C	Hetero	INTRON
SBS	Chr11	2630935	C-T	Hetero	INTERGENIC
SBS	Chr11	7076595	A-T	Hetero	INTERGENIC
SBS	Chr11	7497439	C-T	Hetero	INTERGENIC
SBS	Chr11	7624368	G-T	Hetero	INTERGENIC
SBS	Chr11	12020299	T-C	Hetero	INTRON
SBS	Chr11	24376667	G-A	Hetero	INTERGENIC
SBS	Chr11	27298642	G-A	Hetero	INTERGENIC
SBS	Chr12	4910705	C-T	Hetero	INTERGENIC
SBS	Chr12	5171150	G-C	Homo	INTRON
SBS	Chr12	8336987	C-T	Homo	INTRON
SBS	Chr12	15166941	C-G	Hetero	INTERGENIC
SBS	Chr12	21519852	A-C	Hetero	INTERGENIC

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr10	1573313	1573314	1
Deletion	Chr6	2623780	2623785	5
Deletion	Chr11	5687568	5687573	5
Deletion	Chr4	11159001	11187000	27999
Deletion	Chr7	11272458	11272461	3
Deletion	Chr11	11795885	11795887	2
Deletion	Chr2	15133001	15143000	9999
Deletion	Chr10	16009693	16009695	2
Deletion	Chr2	19002650	19002652	2	OsKitaake02g186101
Deletion	Chr2	19196001	19279000	82999	8
Deletion	Chr3	19222860	19222864	4
Deletion	Chr2	19363001	19416000	52999	5
Deletion	Chr7	20057315	20057319	4
Deletion	Chr2	23637975	23637980	5
Deletion	Chr1	25378982	25378988	6
Deletion	Chr1	26171001	26347000	175999	16
Deletion	Chr2	27499311	27499316	5
Deletion	Chr2	29598877	29598889	12
Deletion	Chr2	29763889	29763890	1
Deletion	Chr1	33153903	33153905	2	OsKitaake01g338400
Deletion	Chr4	34779212	34779220	8
Deletion	Chr1	41760844	41760852	8

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr2	19274903	19288388

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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