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Mutant Information

Mutant Name	FN1299-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN1299-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) = Low (Between 25% and 74%) TO:0000639 (Seed fertility) = Normal (Between 75% and 125%) For more information, please see this phenotype file

Variant Information

Single base substitutions: 30

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 9979163 T-C Homo INTRON
SBS Chr1 15097049 C-G Homo INTRON
SBS Chr2 17570518 C-T Hetero INTERGENIC
SBS Chr2 25638857 G-A Hetero INTERGENIC
SBS Chr2 30073865 G-C Homo INTERGENIC
SBS Chr3 3289492 C-A Homo NON_SYNONYMOUS_CODING OsKitaake03g046400
SBS Chr3 15938058 A-G Hetero INTRON
SBS Chr4 18262610 G-T Homo INTERGENIC
SBS Chr5 484666 A-G Hetero INTERGENIC
SBS Chr5 10561397 C-G Hetero INTERGENIC
SBS Chr6 3698731 G-A Homo UTR_3_PRIME
SBS Chr6 3698732 T-A Homo UTR_3_PRIME
SBS Chr6 7199284 T-A Hetero UTR_3_PRIME
SBS Chr6 15254465 C-A Hetero INTERGENIC
SBS Chr6 15254466 G-A Hetero INTERGENIC
SBS Chr7 17598512 G-A Homo INTERGENIC
SBS Chr8 9742110 A-T Hetero INTERGENIC
SBS Chr8 11158401 G-A Hetero INTERGENIC
SBS Chr8 22089042 A-T Homo INTERGENIC
SBS Chr8 25391505 T-C Hetero INTERGENIC
SBS Chr9 9796335 T-C Hetero INTERGENIC
SBS Chr9 14189982 A-G Homo INTERGENIC
SBS Chr9 17365432 C-T Homo INTERGENIC
SBS Chr10 3636312 A-T Homo INTERGENIC
SBS Chr11 6066121 T-A Hetero INTERGENIC
SBS Chr11 11510632 G-A Hetero INTERGENIC
SBS Chr11 13816582 C-A Hetero INTERGENIC
SBS Chr11 22413497 A-G Homo INTRON
SBS Chr12 16659689 T-A Homo INTERGENIC
SBS Chr12 22575863 T-C Homo INTERGENIC

Deletions: 12

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr6 107143 107144 1
Deletion Chr11 646099 646103 4
Deletion Chr7 2850971 2851292 321
Deletion Chr10 10872699 10872824 125
Deletion Chr10 12047007 12047016 9
Deletion Chr11 14104560 14104562 2 OsKitaake11g117800
Deletion Chr10 17189241 17189247 6
Deletion Chr3 17361042 17361124 82
Deletion Chr6 17969840 17969845 5
Deletion Chr9 18650537 18650539 2 OsKitaake09g147400
Deletion Chr11 24342192 24342230 38
Deletion Chr6 27317001 27325000 7999 OsKitaake06g246000

Insertions: 3

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr3 35237573 35237581 7
Insertion Chr8 11486230 11486233 2
Insertion Chr12 10596599 10596602 2

Inversions: 4

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Inversion Chr5 22010636 22406764 OsKitaake05g179500
Inversion Chr5 22010662 22406764 OsKitaake05g179500
Inversion Chr6 24065321 24585102 OsKitaake06g217900
Inversion Chr6 24476822 24585105 2

Translocations: 2

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes

Translocation Chr4 2762455 Chr2 37131202 OsKitaake02g398800
Translocation Chr6 17444808 Chr2 37131189 OsKitaake02g398800

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	9979163	T-C	Homo	INTRON
SBS	Chr1	15097049	C-G	Homo	INTRON
SBS	Chr2	17570518	C-T	Hetero	INTERGENIC
SBS	Chr2	25638857	G-A	Hetero	INTERGENIC
SBS	Chr2	30073865	G-C	Homo	INTERGENIC
SBS	Chr3	3289492	C-A	Homo	NON_SYNONYMOUS_CODING	OsKitaake03g046400
SBS	Chr3	15938058	A-G	Hetero	INTRON
SBS	Chr4	18262610	G-T	Homo	INTERGENIC
SBS	Chr5	484666	A-G	Hetero	INTERGENIC
SBS	Chr5	10561397	C-G	Hetero	INTERGENIC
SBS	Chr6	3698731	G-A	Homo	UTR_3_PRIME
SBS	Chr6	3698732	T-A	Homo	UTR_3_PRIME
SBS	Chr6	7199284	T-A	Hetero	UTR_3_PRIME
SBS	Chr6	15254465	C-A	Hetero	INTERGENIC
SBS	Chr6	15254466	G-A	Hetero	INTERGENIC
SBS	Chr7	17598512	G-A	Homo	INTERGENIC
SBS	Chr8	9742110	A-T	Hetero	INTERGENIC
SBS	Chr8	11158401	G-A	Hetero	INTERGENIC
SBS	Chr8	22089042	A-T	Homo	INTERGENIC
SBS	Chr8	25391505	T-C	Hetero	INTERGENIC
SBS	Chr9	9796335	T-C	Hetero	INTERGENIC
SBS	Chr9	14189982	A-G	Homo	INTERGENIC
SBS	Chr9	17365432	C-T	Homo	INTERGENIC
SBS	Chr10	3636312	A-T	Homo	INTERGENIC
SBS	Chr11	6066121	T-A	Hetero	INTERGENIC
SBS	Chr11	11510632	G-A	Hetero	INTERGENIC
SBS	Chr11	13816582	C-A	Hetero	INTERGENIC
SBS	Chr11	22413497	A-G	Homo	INTRON
SBS	Chr12	16659689	T-A	Homo	INTERGENIC
SBS	Chr12	22575863	T-C	Homo	INTERGENIC

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr6	107143	107144	1
Deletion	Chr11	646099	646103	4
Deletion	Chr7	2850971	2851292	321
Deletion	Chr10	10872699	10872824	125
Deletion	Chr10	12047007	12047016	9
Deletion	Chr11	14104560	14104562	2	OsKitaake11g117800
Deletion	Chr10	17189241	17189247	6
Deletion	Chr3	17361042	17361124	82
Deletion	Chr6	17969840	17969845	5
Deletion	Chr9	18650537	18650539	2	OsKitaake09g147400
Deletion	Chr11	24342192	24342230	38
Deletion	Chr6	27317001	27325000	7999	OsKitaake06g246000

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr5	22010636	22406764	OsKitaake05g179500
Inversion	Chr5	22010662	22406764	OsKitaake05g179500
Inversion	Chr6	24065321	24585102	OsKitaake06g217900
Inversion	Chr6	24476822	24585105	2

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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