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Mutant Information

Mutant Name	FN-9 [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN-9 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) = 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: 33

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 4257600 G-A Hetero INTRON
SBS Chr1 4686399 C-T Hetero NON_SYNONYMOUS_CODING OsKitaake01g062800
SBS Chr1 31812987 G-T Homo NON_SYNONYMOUS_CODING OsKitaake01g319800
SBS Chr1 32044856 T-A Homo INTERGENIC
SBS Chr2 10840242 T-C Hetero INTERGENIC
SBS Chr2 11511342 T-A Hetero INTERGENIC
SBS Chr2 11511343 C-A Hetero INTERGENIC
SBS Chr2 28131279 C-T Homo INTERGENIC
SBS Chr2 29061079 G-A Homo INTERGENIC
SBS Chr3 4316352 G-A Hetero NON_SYNONYMOUS_CODING OsKitaake03g062000
SBS Chr3 5390855 T-A Hetero UTR_5_PRIME
SBS Chr3 6797915 C-G Hetero NON_SYNONYMOUS_CODING OsKitaake03g096400
SBS Chr3 11602542 G-A Hetero INTERGENIC
SBS Chr4 1820197 C-A Homo INTERGENIC
SBS Chr5 5717861 G-T Homo STOP_GAINED OsKitaake05g060900
SBS Chr5 7917253 G-C Hetero INTERGENIC
SBS Chr5 7917254 G-T Hetero INTERGENIC
SBS Chr5 11236686 T-A Homo INTERGENIC
SBS Chr6 27999598 G-T Homo NON_SYNONYMOUS_CODING OsKitaake06g254300
SBS Chr7 4305872 T-A Homo INTERGENIC
SBS Chr7 4499133 T-A Homo INTERGENIC
SBS Chr7 4499134 G-T Homo INTERGENIC
SBS Chr7 18106203 G-A Hetero INTRON
SBS Chr7 27967026 G-T Homo NON_SYNONYMOUS_CODING OsKitaake07g263200
SBS Chr8 16409951 T-G Hetero INTERGENIC
SBS Chr9 3811133 T-C Hetero INTERGENIC
SBS Chr9 12870297 C-T Hetero INTERGENIC
SBS Chr9 14675636 C-T Hetero NON_SYNONYMOUS_CODING OsKitaake09g100400
SBS Chr10 6669890 T-C Hetero INTERGENIC
SBS Chr10 6669892 T-C Hetero INTERGENIC
SBS Chr11 11503379 G-A Homo INTERGENIC
SBS Chr11 22755612 G-C Hetero NON_SYNONYMOUS_CODING OsKitaake11g180500
SBS Chr12 13452525 A-G Homo INTERGENIC

Deletions: 22

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr6 88291 88645 354
Deletion Chr7 4306098 4306099 1
Deletion Chr9 7681598 7681708 110
Deletion Chr4 8369001 8744000 374999 14
Deletion Chr11 12023719 12023726 7
Deletion Chr9 12386001 12398000 11999 OsKitaake09g080900
Deletion Chr1 13882941 13882947 6
Deletion Chr11 14503990 14504000 10
Deletion Chr5 18230551 18230554 3
Deletion Chr2 18388889 18388890 1 OsKitaake02g182100
Deletion Chr2 19020142 19020220 78
Deletion Chr7 21116364 21116370 6
Deletion Chr1 22725741 22725742 1
Deletion Chr1 22866412 22866423 11
Deletion Chr10 23063019 23063020 1
Deletion Chr6 23444694 23444695 1
Deletion Chr6 23507529 23507530 1
Deletion Chr8 24383652 24383653 1
Deletion Chr6 24767860 24767862 2
Deletion Chr11 27412234 27412236 2
Deletion Chr4 33660321 33660323 2
Deletion Chr3 35605482 35605494 12 OsKitaake03g390700

Insertions: 1

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr1 22530528 22530531 2

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	4257600	G-A	Hetero	INTRON
SBS	Chr1	4686399	C-T	Hetero	NON_SYNONYMOUS_CODING	OsKitaake01g062800
SBS	Chr1	31812987	G-T	Homo	NON_SYNONYMOUS_CODING	OsKitaake01g319800
SBS	Chr1	32044856	T-A	Homo	INTERGENIC
SBS	Chr2	10840242	T-C	Hetero	INTERGENIC
SBS	Chr2	11511342	T-A	Hetero	INTERGENIC
SBS	Chr2	11511343	C-A	Hetero	INTERGENIC
SBS	Chr2	28131279	C-T	Homo	INTERGENIC
SBS	Chr2	29061079	G-A	Homo	INTERGENIC
SBS	Chr3	4316352	G-A	Hetero	NON_SYNONYMOUS_CODING	OsKitaake03g062000
SBS	Chr3	5390855	T-A	Hetero	UTR_5_PRIME
SBS	Chr3	6797915	C-G	Hetero	NON_SYNONYMOUS_CODING	OsKitaake03g096400
SBS	Chr3	11602542	G-A	Hetero	INTERGENIC
SBS	Chr4	1820197	C-A	Homo	INTERGENIC
SBS	Chr5	5717861	G-T	Homo	STOP_GAINED	OsKitaake05g060900
SBS	Chr5	7917253	G-C	Hetero	INTERGENIC
SBS	Chr5	7917254	G-T	Hetero	INTERGENIC
SBS	Chr5	11236686	T-A	Homo	INTERGENIC
SBS	Chr6	27999598	G-T	Homo	NON_SYNONYMOUS_CODING	OsKitaake06g254300
SBS	Chr7	4305872	T-A	Homo	INTERGENIC
SBS	Chr7	4499133	T-A	Homo	INTERGENIC
SBS	Chr7	4499134	G-T	Homo	INTERGENIC
SBS	Chr7	18106203	G-A	Hetero	INTRON
SBS	Chr7	27967026	G-T	Homo	NON_SYNONYMOUS_CODING	OsKitaake07g263200
SBS	Chr8	16409951	T-G	Hetero	INTERGENIC
SBS	Chr9	3811133	T-C	Hetero	INTERGENIC
SBS	Chr9	12870297	C-T	Hetero	INTERGENIC
SBS	Chr9	14675636	C-T	Hetero	NON_SYNONYMOUS_CODING	OsKitaake09g100400
SBS	Chr10	6669890	T-C	Hetero	INTERGENIC
SBS	Chr10	6669892	T-C	Hetero	INTERGENIC
SBS	Chr11	11503379	G-A	Homo	INTERGENIC
SBS	Chr11	22755612	G-C	Hetero	NON_SYNONYMOUS_CODING	OsKitaake11g180500
SBS	Chr12	13452525	A-G	Homo	INTERGENIC

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr6	88291	88645	354
Deletion	Chr7	4306098	4306099	1
Deletion	Chr9	7681598	7681708	110
Deletion	Chr4	8369001	8744000	374999	14
Deletion	Chr11	12023719	12023726	7
Deletion	Chr9	12386001	12398000	11999	OsKitaake09g080900
Deletion	Chr1	13882941	13882947	6
Deletion	Chr11	14503990	14504000	10
Deletion	Chr5	18230551	18230554	3
Deletion	Chr2	18388889	18388890	1	OsKitaake02g182100
Deletion	Chr2	19020142	19020220	78
Deletion	Chr7	21116364	21116370	6
Deletion	Chr1	22725741	22725742	1
Deletion	Chr1	22866412	22866423	11
Deletion	Chr10	23063019	23063020	1
Deletion	Chr6	23444694	23444695	1
Deletion	Chr6	23507529	23507530	1
Deletion	Chr8	24383652	24383653	1
Deletion	Chr6	24767860	24767862	2
Deletion	Chr11	27412234	27412236	2
Deletion	Chr4	33660321	33660323	2
Deletion	Chr3	35605482	35605494	12	OsKitaake03g390700

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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