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Mutant Information

Mutant Name	W246-5-1 [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download W246-5-1 Alignment File
Seed Availability	No
Phenotype	TO:0000014 (Panicle Weight) = Very Low (below 24% compare to WT) TO:0000207 (Plant height) = Normal (Between 75% and 125%) TO:0000445 (Seed Number) = Low (Between 25% and 74%) TO:0000639 (Seed fertility) = Low (Between 25% and 74%) For more information, please see this phenotype file

Variant Information

Single base substitutions: 45

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	2061289	C-A	Homo	INTERGENIC
SBS	Chr1	14324616	A-T	Homo	INTERGENIC
SBS	Chr1	17681089	G-A	Homo	INTRON
SBS	Chr1	21616904	C-A	Homo	INTERGENIC
SBS	Chr1	24509482	A-T	Homo	INTRON
SBS	Chr1	24509483	G-T	Homo	INTRON
SBS	Chr2	1274964	G-C	Hetero	INTERGENIC
SBS	Chr2	31850398	C-T	Hetero	INTERGENIC
SBS	Chr2	35940162	C-T	Homo	INTERGENIC
SBS	Chr3	6673601	A-C	Homo	INTERGENIC
SBS	Chr3	13738887	G-T	Homo	INTERGENIC
SBS	Chr3	13738888	C-T	Homo	INTERGENIC
SBS	Chr3	27564418	T-C	Homo	INTERGENIC
SBS	Chr4	65166	C-T	Hetero	SYNONYMOUS_CODING
SBS	Chr4	21255097	A-G	Hetero	INTERGENIC
SBS	Chr4	23823096	G-T	Hetero	UTR_5_PRIME
SBS	Chr5	387664	C-T	Hetero	INTERGENIC
SBS	Chr5	1745516	T-A	Hetero	INTERGENIC
SBS	Chr5	5903414	C-G	Hetero	INTERGENIC
SBS	Chr5	8677474	G-A	Homo	INTERGENIC
SBS	Chr6	28904439	C-T	Homo	INTERGENIC
SBS	Chr7	10529822	C-T	Homo	INTERGENIC
SBS	Chr7	23036277	A-T	Homo	UTR_3_PRIME
SBS	Chr8	9501657	T-G	Hetero	INTERGENIC
SBS	Chr8	17809785	A-G	Hetero	UTR_3_PRIME
SBS	Chr8	23924411	C-T	Homo	INTERGENIC
SBS	Chr8	28199226	T-A	Hetero	INTERGENIC
SBS	Chr8	28199227	C-A	Hetero	INTERGENIC
SBS	Chr8	28199228	T-A	Hetero	INTERGENIC
SBS	Chr9	5934305	G-T	Homo	INTERGENIC
SBS	Chr9	21216430	G-A	Homo	INTERGENIC
SBS	Chr9	22211796	T-A	Hetero	INTERGENIC
SBS	Chr11	11205484	G-T	Homo	INTERGENIC
SBS	Chr11	16846241	C-T	Hetero	INTERGENIC
SBS	Chr11	18391810	C-G	Homo	NON_SYNONYMOUS_CODING	OsKitaake11g142801
SBS	Chr11	25507513	T-A	Homo	UTR_3_PRIME
SBS	Chr12	2970185	C-T	Homo	INTERGENIC
SBS	Chr12	3243253	A-G	Homo	INTERGENIC
SBS	Chr12	5480022	C-T	Hetero	INTERGENIC
SBS	Chr12	15666809	G-C	Homo	INTERGENIC
SBS	Chr12	15748057	C-T	Homo	INTERGENIC
SBS	Chr12	15748059	A-T	Homo	INTERGENIC
SBS	Chr12	15748062	C-T	Homo	INTERGENIC
SBS	Chr12	16722322	T-C	Hetero	INTERGENIC
SBS	Chr12	23978893	A-C	Hetero	INTERGENIC

Deletions: 24

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr8	594926	594931	5
Deletion	Chr9	1649102	1649104	2
Deletion	Chr9	2879396	2879397	1
Deletion	Chr7	4721797	4721799	2
Deletion	Chr7	4742180	4742305	125
Deletion	Chr2	9323333	9323334	1
Deletion	Chr5	10119539	10119541	2	OsKitaake05g089901
Deletion	Chr10	10647213	10647214	1
Deletion	Chr10	11110373	11110392	19
Deletion	Chr9	14412266	14412595	329
Deletion	Chr12	15559187	15559201	14
Deletion	Chr5	15608772	15608773	1
Deletion	Chr6	16208274	16208339	65	OsKitaake06g155500
Deletion	Chr6	17011424	17011435	11
Deletion	Chr5	18413320	18413327	7
Deletion	Chr12	18463032	18463045	13
Deletion	Chr10	18577918	18577936	18
Deletion	Chr6	19641525	19641526	1
Deletion	Chr6	20015088	20015089	1
Deletion	Chr6	20805300	20805315	15
Deletion	Chr11	22085564	22085565	1
Deletion	Chr8	23228001	23241000	12999	3
Deletion	Chr4	32708100	32708106	6
Deletion	Chr1	43405001	43409000	3999	OsKitaake01g480500

Insertions: 1

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Insertion	Chr12	3585267	3585269	1

Inversions: 8

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr11	11145291	11489292
Inversion	Chr12	14500910	14824339	OsKitaake12g116200
Inversion	Chr12	14824354	15709328
Inversion	Chr12	15203036	15709328
Inversion	Chr8	16209295	16736584
Inversion	Chr8	16209300	16736585
Inversion	Chr1	43404578	43823901	OsKitaake01g480500
Inversion	Chr1	43409762	43711973	2

Translocations: 5

Variant Type	Chromosome	Position 1	Chromosome	Position 2	Number of Genes
Translocation	Chr6	5724249	Chr1	43648812	OsKitaake06g075100
Translocation	Chr12	14500913	Chr6	5718923	2
Translocation	Chr12	15203130	Chr1	43648288	OsKitaake01g484900
Translocation	Chr4	32068116	Chr1	43711968	2
Translocation	Chr4	32068196	Chr1	43710994	2

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Variant Type

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Change

Genotype

Effect

Gene Affected

Variant Type

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End

Size(bp)

Number of Genes

Variant Type

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Size(bp)

Number of Genes

Variant Type

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Number of Genes

Variant Type

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Number of Genes