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Mutant Information

Mutant Name	FN2499 [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN2499 Alignment File
Seed Availability	Yes [Order Seeds]
Phenotype	TO:0000430 (Germination Rate) = Normal (Between 75% and 125%) For more information, please see this phenotype file

Variant Information

Single base substitutions: 37

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 2321962 G-A Hetero UTR_3_PRIME
SBS Chr1 3989125 G-A Hetero UTR_5_PRIME
SBS Chr1 10656967 G-A Homo INTERGENIC
SBS Chr1 29417230 G-A Hetero INTERGENIC
SBS Chr1 33098090 A-C Hetero INTERGENIC
SBS Chr1 33910750 C-A Hetero INTERGENIC
SBS Chr1 43854245 G-A Hetero INTERGENIC
SBS Chr2 107336 A-T Hetero INTRON
SBS Chr2 28249138 G-T Hetero INTERGENIC
SBS Chr3 8790571 G-A Hetero INTERGENIC
SBS Chr3 14317392 C-G Homo INTERGENIC
SBS Chr4 27147619 G-A Hetero INTERGENIC
SBS Chr5 3774030 T-C Homo INTRON
SBS Chr5 23782347 C-T Homo UTR_3_PRIME
SBS Chr5 24037272 C-T Homo INTRON
SBS Chr5 27328469 T-C Homo INTERGENIC
SBS Chr6 11564966 C-T Homo INTERGENIC
SBS Chr6 13386980 G-A Homo INTERGENIC
SBS Chr6 24209770 G-A Homo INTERGENIC
SBS Chr7 13744335 C-T Homo INTERGENIC
SBS Chr7 25472482 G-C Hetero INTERGENIC
SBS Chr7 26525670 C-T Homo NON_SYNONYMOUS_CODING OsKitaake07g245500
SBS Chr8 12964834 G-A Homo INTERGENIC
SBS Chr8 21040485 A-T Homo INTERGENIC
SBS Chr8 27530141 T-A Hetero INTERGENIC
SBS Chr9 65163 A-C Hetero INTERGENIC
SBS Chr9 6132646 C-A Homo INTERGENIC
SBS Chr9 8095069 T-A Hetero INTERGENIC
SBS Chr9 8309397 C-G Hetero INTERGENIC
SBS Chr9 14419676 G-A Hetero UTR_3_PRIME
SBS Chr10 3745994 T-A Homo INTERGENIC
SBS Chr10 3745995 C-A Homo INTERGENIC
SBS Chr11 11724752 T-A Hetero INTRON
SBS Chr11 19729917 C-T Hetero INTERGENIC
SBS Chr11 19782951 A-T Hetero INTRON
SBS Chr12 9350714 C-T Hetero INTERGENIC
SBS Chr12 9350845 A-G Hetero INTERGENIC

Deletions: 15

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr4 1379092 1379095 3
Deletion Chr8 7650501 7650504 3
Deletion Chr8 11678970 11678972 2
Deletion Chr12 11806001 11831000 24999
Deletion Chr10 14629779 14629780 1
Deletion Chr9 15084997 15085003 6
Deletion Chr9 17282001 17314000 31999 4
Deletion Chr6 19125021 19125033 12
Deletion Chr3 20293891 20293892 1
Deletion Chr1 22146001 22162000 15999 OsKitaake01g211800
Deletion Chr5 27732395 27732398 3
Deletion Chr3 28739361 28739365 4
Deletion Chr3 31268327 31268328 1
Deletion Chr4 31731964 31731973 9
Deletion Chr1 41337501 41337507 6

Insertions: 4

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr1 18354747 18354750 2
Insertion Chr7 12638172 12638177 4
Insertion Chr8 27703245 27703248 2
Insertion Chr11 5035523 5035526 2

Inversions: 5

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Inversion Chr6 14838376 15494150
Inversion Chr9 17282223 18007491
Inversion Chr9 17318596 18007501
Inversion Chr8 22791278 23392164 2
Inversion Chr8 22791288 23392165 2

Translocations: 1

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes

Translocation Chr12 11854141 Chr6 15494145 OsKitaake12g103700

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	2321962	G-A	Hetero	UTR_3_PRIME
SBS	Chr1	3989125	G-A	Hetero	UTR_5_PRIME
SBS	Chr1	10656967	G-A	Homo	INTERGENIC
SBS	Chr1	29417230	G-A	Hetero	INTERGENIC
SBS	Chr1	33098090	A-C	Hetero	INTERGENIC
SBS	Chr1	33910750	C-A	Hetero	INTERGENIC
SBS	Chr1	43854245	G-A	Hetero	INTERGENIC
SBS	Chr2	107336	A-T	Hetero	INTRON
SBS	Chr2	28249138	G-T	Hetero	INTERGENIC
SBS	Chr3	8790571	G-A	Hetero	INTERGENIC
SBS	Chr3	14317392	C-G	Homo	INTERGENIC
SBS	Chr4	27147619	G-A	Hetero	INTERGENIC
SBS	Chr5	3774030	T-C	Homo	INTRON
SBS	Chr5	23782347	C-T	Homo	UTR_3_PRIME
SBS	Chr5	24037272	C-T	Homo	INTRON
SBS	Chr5	27328469	T-C	Homo	INTERGENIC
SBS	Chr6	11564966	C-T	Homo	INTERGENIC
SBS	Chr6	13386980	G-A	Homo	INTERGENIC
SBS	Chr6	24209770	G-A	Homo	INTERGENIC
SBS	Chr7	13744335	C-T	Homo	INTERGENIC
SBS	Chr7	25472482	G-C	Hetero	INTERGENIC
SBS	Chr7	26525670	C-T	Homo	NON_SYNONYMOUS_CODING	OsKitaake07g245500
SBS	Chr8	12964834	G-A	Homo	INTERGENIC
SBS	Chr8	21040485	A-T	Homo	INTERGENIC
SBS	Chr8	27530141	T-A	Hetero	INTERGENIC
SBS	Chr9	65163	A-C	Hetero	INTERGENIC
SBS	Chr9	6132646	C-A	Homo	INTERGENIC
SBS	Chr9	8095069	T-A	Hetero	INTERGENIC
SBS	Chr9	8309397	C-G	Hetero	INTERGENIC
SBS	Chr9	14419676	G-A	Hetero	UTR_3_PRIME
SBS	Chr10	3745994	T-A	Homo	INTERGENIC
SBS	Chr10	3745995	C-A	Homo	INTERGENIC
SBS	Chr11	11724752	T-A	Hetero	INTRON
SBS	Chr11	19729917	C-T	Hetero	INTERGENIC
SBS	Chr11	19782951	A-T	Hetero	INTRON
SBS	Chr12	9350714	C-T	Hetero	INTERGENIC
SBS	Chr12	9350845	A-G	Hetero	INTERGENIC

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr4	1379092	1379095	3
Deletion	Chr8	7650501	7650504	3
Deletion	Chr8	11678970	11678972	2
Deletion	Chr12	11806001	11831000	24999
Deletion	Chr10	14629779	14629780	1
Deletion	Chr9	15084997	15085003	6
Deletion	Chr9	17282001	17314000	31999	4
Deletion	Chr6	19125021	19125033	12
Deletion	Chr3	20293891	20293892	1
Deletion	Chr1	22146001	22162000	15999	OsKitaake01g211800
Deletion	Chr5	27732395	27732398	3
Deletion	Chr3	28739361	28739365	4
Deletion	Chr3	31268327	31268328	1
Deletion	Chr4	31731964	31731973	9
Deletion	Chr1	41337501	41337507	6

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr6	14838376	15494150
Inversion	Chr9	17282223	18007491
Inversion	Chr9	17318596	18007501
Inversion	Chr8	22791278	23392164	2
Inversion	Chr8	22791288	23392165	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