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Mutant Information

Mutant Name	FN1458-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN1458-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) = Low (Between 25% and 75%) For more information, please see this phenotype file

Variant Information

Single base substitutions: 40

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 32525334 C-A Hetero INTRON
SBS Chr1 42902399 G-A Homo INTERGENIC
SBS Chr2 7112167 C-T Hetero INTRON
SBS Chr2 17836920 C-A Hetero INTERGENIC
SBS Chr2 29533340 G-A Hetero INTERGENIC
SBS Chr2 36059310 C-T Hetero NON_SYNONYMOUS_CODING OsKitaake02g380000
SBS Chr2 36059311 T-C Hetero SYNONYMOUS_CODING
SBS Chr3 12706626 C-T Homo INTERGENIC
SBS Chr3 27192811 G-A Hetero INTERGENIC
SBS Chr3 33529961 G-C Homo INTRON
SBS Chr4 1357053 G-A Hetero INTERGENIC
SBS Chr4 10673427 C-T Hetero INTERGENIC
SBS Chr4 13892538 A-G Hetero INTERGENIC
SBS Chr4 14052534 G-A Hetero INTERGENIC
SBS Chr4 18446988 C-A Homo INTERGENIC
SBS Chr4 19292889 T-G Hetero INTERGENIC
SBS Chr5 18519830 C-T Hetero INTERGENIC
SBS Chr5 24090544 C-T Homo INTERGENIC
SBS Chr5 24899122 T-A Homo INTRON
SBS Chr6 2848594 A-T Homo INTERGENIC
SBS Chr6 11125833 G-A Hetero INTERGENIC
SBS Chr6 11597910 T-A Hetero INTERGENIC
SBS Chr6 17600797 G-A Hetero INTERGENIC
SBS Chr6 27970236 G-T Hetero INTERGENIC
SBS Chr7 15921295 C-T Hetero INTERGENIC
SBS Chr7 15935211 C-T Hetero INTERGENIC
SBS Chr8 5222931 C-A Hetero INTERGENIC
SBS Chr8 13866166 G-C Hetero INTERGENIC
SBS Chr8 14234639 C-A Homo INTERGENIC
SBS Chr8 25847697 T-G Hetero INTERGENIC
SBS Chr9 3117445 T-A Hetero UTR_3_PRIME
SBS Chr9 4144216 G-A Hetero INTERGENIC
SBS Chr9 8280589 G-A Hetero INTERGENIC
SBS Chr11 5930359 C-T Homo INTRON
SBS Chr11 6927612 G-C Hetero INTERGENIC
SBS Chr11 11167776 C-T Homo INTERGENIC
SBS Chr11 15207663 G-A Hetero INTERGENIC
SBS Chr12 13828721 G-A Hetero INTRON
SBS Chr12 16822019 G-T Hetero INTERGENIC
SBS Chr12 23925877 A-G Homo INTERGENIC

Deletions: 46

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr3 171001 185000 13999 4
Deletion Chr10 326964 326966 2 OsKitaake10g002200
Deletion Chr1 371001 381000 9999 OsKitaake01g005200
Deletion Chr5 575001 597000 21999 3
Deletion Chr2 598001 614000 15999 OsKitaake02g009000
Deletion Chr3 1087001 1106000 18999 OsKitaake03g016901
Deletion Chr5 1444001 1456000 11999 2
Deletion Chr9 1601001 1613000 11999 OsKitaake09g009200
Deletion Chr7 1657001 1671000 13999 5
Deletion Chr7 1790001 1804000 13999 OsKitaake07g025200
Deletion Chr11 2787309 2787325 16
Deletion Chr2 3189001 3203000 13999 5
Deletion Chr9 3585917 3586098 181
Deletion Chr1 3646001 3658000 11999 OsKitaake01g049000
Deletion Chr7 4078438 4078442 4
Deletion Chr4 4959001 4972000 12999 OsKitaake04g022400
Deletion Chr8 5421001 5445000 23999 4
Deletion Chr9 6146502 6146510 8
Deletion Chr7 6216001 6233000 16999 2
Deletion Chr2 6852886 6852888 2
Deletion Chr9 6939001 6951000 11999 OsKitaake09g039700
Deletion Chr1 10032587 10032588 1
Deletion Chr12 10442001 10454000 11999 3
Deletion Chr6 11482001 11497000 14999 OsKitaake06g126800
Deletion Chr6 11566775 11566777 2
Deletion Chr5 12511001 12559000 47999
Deletion Chr2 12747001 12762000 14999 4
Deletion Chr10 15185001 15194000 8999 3
Deletion Chr5 15256613 15256620 7
Deletion Chr2 16072001 16100000 27999 OsKitaake02g166300
Deletion Chr11 16337944 16337946 2
Deletion Chr6 17567001 17580000 12999 2
Deletion Chr9 19574001 19589000 14999 2
Deletion Chr7 21296447 21296448 1
Deletion Chr1 21548001 21575000 26999
Deletion Chr7 22163279 22163281 2
Deletion Chr3 23756001 23759000 2999 OsKitaake03g255300
Deletion Chr12 23807001 23820000 12999 OsKitaake12g191766
Deletion Chr12 23947750 23947754 4
Deletion Chr12 24378001 24399000 20999 3
Deletion Chr11 24528001 24543000 14999 OsKitaake11g197800
Deletion Chr11 25115001 25125000 9999 2
Deletion Chr5 27534837 27534845 8
Deletion Chr8 28304244 28304246 2
Deletion Chr3 28651001 28665000 13999
Deletion Chr1 41462001 41483000 20999 OsKitaake01g452800

Insertions: 10

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr1 39475423 39475426 2
Insertion Chr4 5441273 5441276 2
Insertion Chr4 15647487 15647490 2
Insertion Chr4 30445616 30445621 4
Insertion Chr5 6760517 6760520 2
Insertion Chr8 14127168 14127173 4
Insertion Chr9 387232 387243 10
Insertion Chr9 11076411 11076413 1
Insertion Chr10 10450305 10450310 4
Insertion Chr7 8498072 8498074 1

Inversions: 2

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Inversion Chr6 26036460 26316889 OsKitaake06g235900
Inversion Chr6 26036473 26316887 OsKitaake06g235900

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	32525334	C-A	Hetero	INTRON
SBS	Chr1	42902399	G-A	Homo	INTERGENIC
SBS	Chr2	7112167	C-T	Hetero	INTRON
SBS	Chr2	17836920	C-A	Hetero	INTERGENIC
SBS	Chr2	29533340	G-A	Hetero	INTERGENIC
SBS	Chr2	36059310	C-T	Hetero	NON_SYNONYMOUS_CODING	OsKitaake02g380000
SBS	Chr2	36059311	T-C	Hetero	SYNONYMOUS_CODING
SBS	Chr3	12706626	C-T	Homo	INTERGENIC
SBS	Chr3	27192811	G-A	Hetero	INTERGENIC
SBS	Chr3	33529961	G-C	Homo	INTRON
SBS	Chr4	1357053	G-A	Hetero	INTERGENIC
SBS	Chr4	10673427	C-T	Hetero	INTERGENIC
SBS	Chr4	13892538	A-G	Hetero	INTERGENIC
SBS	Chr4	14052534	G-A	Hetero	INTERGENIC
SBS	Chr4	18446988	C-A	Homo	INTERGENIC
SBS	Chr4	19292889	T-G	Hetero	INTERGENIC
SBS	Chr5	18519830	C-T	Hetero	INTERGENIC
SBS	Chr5	24090544	C-T	Homo	INTERGENIC
SBS	Chr5	24899122	T-A	Homo	INTRON
SBS	Chr6	2848594	A-T	Homo	INTERGENIC
SBS	Chr6	11125833	G-A	Hetero	INTERGENIC
SBS	Chr6	11597910	T-A	Hetero	INTERGENIC
SBS	Chr6	17600797	G-A	Hetero	INTERGENIC
SBS	Chr6	27970236	G-T	Hetero	INTERGENIC
SBS	Chr7	15921295	C-T	Hetero	INTERGENIC
SBS	Chr7	15935211	C-T	Hetero	INTERGENIC
SBS	Chr8	5222931	C-A	Hetero	INTERGENIC
SBS	Chr8	13866166	G-C	Hetero	INTERGENIC
SBS	Chr8	14234639	C-A	Homo	INTERGENIC
SBS	Chr8	25847697	T-G	Hetero	INTERGENIC
SBS	Chr9	3117445	T-A	Hetero	UTR_3_PRIME
SBS	Chr9	4144216	G-A	Hetero	INTERGENIC
SBS	Chr9	8280589	G-A	Hetero	INTERGENIC
SBS	Chr11	5930359	C-T	Homo	INTRON
SBS	Chr11	6927612	G-C	Hetero	INTERGENIC
SBS	Chr11	11167776	C-T	Homo	INTERGENIC
SBS	Chr11	15207663	G-A	Hetero	INTERGENIC
SBS	Chr12	13828721	G-A	Hetero	INTRON
SBS	Chr12	16822019	G-T	Hetero	INTERGENIC
SBS	Chr12	23925877	A-G	Homo	INTERGENIC

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr3	171001	185000	13999	4
Deletion	Chr10	326964	326966	2	OsKitaake10g002200
Deletion	Chr1	371001	381000	9999	OsKitaake01g005200
Deletion	Chr5	575001	597000	21999	3
Deletion	Chr2	598001	614000	15999	OsKitaake02g009000
Deletion	Chr3	1087001	1106000	18999	OsKitaake03g016901
Deletion	Chr5	1444001	1456000	11999	2
Deletion	Chr9	1601001	1613000	11999	OsKitaake09g009200
Deletion	Chr7	1657001	1671000	13999	5
Deletion	Chr7	1790001	1804000	13999	OsKitaake07g025200
Deletion	Chr11	2787309	2787325	16
Deletion	Chr2	3189001	3203000	13999	5
Deletion	Chr9	3585917	3586098	181
Deletion	Chr1	3646001	3658000	11999	OsKitaake01g049000
Deletion	Chr7	4078438	4078442	4
Deletion	Chr4	4959001	4972000	12999	OsKitaake04g022400
Deletion	Chr8	5421001	5445000	23999	4
Deletion	Chr9	6146502	6146510	8
Deletion	Chr7	6216001	6233000	16999	2
Deletion	Chr2	6852886	6852888	2
Deletion	Chr9	6939001	6951000	11999	OsKitaake09g039700
Deletion	Chr1	10032587	10032588	1
Deletion	Chr12	10442001	10454000	11999	3
Deletion	Chr6	11482001	11497000	14999	OsKitaake06g126800
Deletion	Chr6	11566775	11566777	2
Deletion	Chr5	12511001	12559000	47999
Deletion	Chr2	12747001	12762000	14999	4
Deletion	Chr10	15185001	15194000	8999	3
Deletion	Chr5	15256613	15256620	7
Deletion	Chr2	16072001	16100000	27999	OsKitaake02g166300
Deletion	Chr11	16337944	16337946	2
Deletion	Chr6	17567001	17580000	12999	2
Deletion	Chr9	19574001	19589000	14999	2
Deletion	Chr7	21296447	21296448	1
Deletion	Chr1	21548001	21575000	26999
Deletion	Chr7	22163279	22163281	2
Deletion	Chr3	23756001	23759000	2999	OsKitaake03g255300
Deletion	Chr12	23807001	23820000	12999	OsKitaake12g191766
Deletion	Chr12	23947750	23947754	4
Deletion	Chr12	24378001	24399000	20999	3
Deletion	Chr11	24528001	24543000	14999	OsKitaake11g197800
Deletion	Chr11	25115001	25125000	9999	2
Deletion	Chr5	27534837	27534845	8
Deletion	Chr8	28304244	28304246	2
Deletion	Chr3	28651001	28665000	13999
Deletion	Chr1	41462001	41483000	20999	OsKitaake01g452800

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr6	26036460	26316889	OsKitaake06g235900
Inversion	Chr6	26036473	26316887	OsKitaake06g235900

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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