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Mutant Information

Mutant Name	FN2500 [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN2500 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: 52

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 9234532 C-A Hetero INTERGENIC
SBS Chr1 9865290 A-T Hetero INTRON
SBS Chr1 10366047 G-A Hetero INTRON
SBS Chr1 29607729 A-T Hetero INTERGENIC
SBS Chr2 12379910 C-T Homo INTRON
SBS Chr2 18198813 T-G Homo INTERGENIC
SBS Chr2 22176564 T-C Hetero INTERGENIC
SBS Chr2 22321313 G-T Hetero INTERGENIC
SBS Chr2 24959094 A-C Hetero INTERGENIC
SBS Chr2 26792208 A-G Hetero INTERGENIC
SBS Chr2 28266699 A-T Hetero INTERGENIC
SBS Chr3 3116601 A-T Hetero INTERGENIC
SBS Chr3 3503547 C-T Hetero INTERGENIC
SBS Chr3 7495630 G-A Hetero INTERGENIC
SBS Chr3 15792833 A-G Homo INTERGENIC
SBS Chr3 15792840 A-C Homo INTERGENIC
SBS Chr3 16673532 C-T Hetero INTERGENIC
SBS Chr3 18451470 A-G Homo UTR_3_PRIME
SBS Chr3 23905524 T-A Homo INTERGENIC
SBS Chr3 25937698 C-T Homo INTERGENIC
SBS Chr3 36095378 A-G Hetero INTERGENIC
SBS Chr4 8713389 A-G Hetero INTRON
SBS Chr4 14320997 G-A Hetero INTERGENIC
SBS Chr4 14596363 G-A Hetero INTERGENIC
SBS Chr4 18501354 C-A Hetero INTERGENIC
SBS Chr4 18556927 G-T Hetero INTRON
SBS Chr4 31948289 A-G Hetero INTERGENIC
SBS Chr4 32491547 A-C Hetero NON_SYNONYMOUS_CODING OsKitaake04g260200
SBS Chr5 6367047 G-A Hetero INTERGENIC
SBS Chr5 23661291 T-A Hetero INTERGENIC
SBS Chr6 11364103 G-A Hetero INTERGENIC
SBS Chr6 20880596 A-G Hetero INTERGENIC
SBS Chr6 21717498 A-G Hetero INTERGENIC
SBS Chr6 22632700 C-T Hetero INTERGENIC
SBS Chr6 23657414 A-G Hetero INTERGENIC
SBS Chr6 26715254 A-G Homo INTERGENIC
SBS Chr6 29636215 T-A Hetero INTERGENIC
SBS Chr7 5349746 C-G Hetero INTERGENIC
SBS Chr7 10382424 C-A Hetero INTERGENIC
SBS Chr7 23216576 C-T Hetero INTERGENIC
SBS Chr7 25480171 T-C Hetero INTRON
SBS Chr8 9950480 T-A Hetero INTRON
SBS Chr8 12680388 A-T Hetero INTERGENIC
SBS Chr8 13581729 G-A Hetero INTERGENIC
SBS Chr9 4846734 C-T Hetero INTERGENIC
SBS Chr9 7493003 C-T Homo UTR_3_PRIME
SBS Chr10 14604710 G-A Hetero INTERGENIC
SBS Chr10 21045050 C-T Hetero INTERGENIC
SBS Chr10 22449762 A-C Homo INTERGENIC
SBS Chr11 12431351 A-C Hetero INTERGENIC
SBS Chr12 7081360 C-T Hetero INTERGENIC
SBS Chr12 9716862 T-A Hetero SYNONYMOUS_CODING

Deletions: 8

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr12 4224436 4224455 19
Deletion Chr11 7218786 7218787 1
Deletion Chr5 7442001 7533000 90999 11
Deletion Chr9 15933260 15933261 1
Deletion Chr5 16055079 16055081 2
Deletion Chr2 17150001 17177000 26999 OsKitaake02g173200
Deletion Chr1 31371325 31371327 2
Deletion Chr2 36708417 36708418 1

Insertions: 5

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr2 4605218 4605221 2
Insertion Chr2 34313697 34313701 3
Insertion Chr4 20490968 20490971 2
Insertion Chr7 15700486 15700489 2
Insertion Chr12 26341626 26341633 6 OsKitaake12g218700

Inversions: 9

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Inversion Chr5 6706720 7532318
Inversion Chr10 6810773 7092328
Inversion Chr10 6810775 7092335
Inversion Chr7 9913989 10086012 2
Inversion Chr7 9913997 10086015 2
Inversion Chr11 10607706 10724448
Inversion Chr11 10607720 10724459
Inversion Chr8 27990801 28086616 OsKitaake08g236100
Inversion Chr8 27990803 28086614 OsKitaake08g236100

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	9234532	C-A	Hetero	INTERGENIC
SBS	Chr1	9865290	A-T	Hetero	INTRON
SBS	Chr1	10366047	G-A	Hetero	INTRON
SBS	Chr1	29607729	A-T	Hetero	INTERGENIC
SBS	Chr2	12379910	C-T	Homo	INTRON
SBS	Chr2	18198813	T-G	Homo	INTERGENIC
SBS	Chr2	22176564	T-C	Hetero	INTERGENIC
SBS	Chr2	22321313	G-T	Hetero	INTERGENIC
SBS	Chr2	24959094	A-C	Hetero	INTERGENIC
SBS	Chr2	26792208	A-G	Hetero	INTERGENIC
SBS	Chr2	28266699	A-T	Hetero	INTERGENIC
SBS	Chr3	3116601	A-T	Hetero	INTERGENIC
SBS	Chr3	3503547	C-T	Hetero	INTERGENIC
SBS	Chr3	7495630	G-A	Hetero	INTERGENIC
SBS	Chr3	15792833	A-G	Homo	INTERGENIC
SBS	Chr3	15792840	A-C	Homo	INTERGENIC
SBS	Chr3	16673532	C-T	Hetero	INTERGENIC
SBS	Chr3	18451470	A-G	Homo	UTR_3_PRIME
SBS	Chr3	23905524	T-A	Homo	INTERGENIC
SBS	Chr3	25937698	C-T	Homo	INTERGENIC
SBS	Chr3	36095378	A-G	Hetero	INTERGENIC
SBS	Chr4	8713389	A-G	Hetero	INTRON
SBS	Chr4	14320997	G-A	Hetero	INTERGENIC
SBS	Chr4	14596363	G-A	Hetero	INTERGENIC
SBS	Chr4	18501354	C-A	Hetero	INTERGENIC
SBS	Chr4	18556927	G-T	Hetero	INTRON
SBS	Chr4	31948289	A-G	Hetero	INTERGENIC
SBS	Chr4	32491547	A-C	Hetero	NON_SYNONYMOUS_CODING	OsKitaake04g260200
SBS	Chr5	6367047	G-A	Hetero	INTERGENIC
SBS	Chr5	23661291	T-A	Hetero	INTERGENIC
SBS	Chr6	11364103	G-A	Hetero	INTERGENIC
SBS	Chr6	20880596	A-G	Hetero	INTERGENIC
SBS	Chr6	21717498	A-G	Hetero	INTERGENIC
SBS	Chr6	22632700	C-T	Hetero	INTERGENIC
SBS	Chr6	23657414	A-G	Hetero	INTERGENIC
SBS	Chr6	26715254	A-G	Homo	INTERGENIC
SBS	Chr6	29636215	T-A	Hetero	INTERGENIC
SBS	Chr7	5349746	C-G	Hetero	INTERGENIC
SBS	Chr7	10382424	C-A	Hetero	INTERGENIC
SBS	Chr7	23216576	C-T	Hetero	INTERGENIC
SBS	Chr7	25480171	T-C	Hetero	INTRON
SBS	Chr8	9950480	T-A	Hetero	INTRON
SBS	Chr8	12680388	A-T	Hetero	INTERGENIC
SBS	Chr8	13581729	G-A	Hetero	INTERGENIC
SBS	Chr9	4846734	C-T	Hetero	INTERGENIC
SBS	Chr9	7493003	C-T	Homo	UTR_3_PRIME
SBS	Chr10	14604710	G-A	Hetero	INTERGENIC
SBS	Chr10	21045050	C-T	Hetero	INTERGENIC
SBS	Chr10	22449762	A-C	Homo	INTERGENIC
SBS	Chr11	12431351	A-C	Hetero	INTERGENIC
SBS	Chr12	7081360	C-T	Hetero	INTERGENIC
SBS	Chr12	9716862	T-A	Hetero	SYNONYMOUS_CODING

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr12	4224436	4224455	19
Deletion	Chr11	7218786	7218787	1
Deletion	Chr5	7442001	7533000	90999	11
Deletion	Chr9	15933260	15933261	1
Deletion	Chr5	16055079	16055081	2
Deletion	Chr2	17150001	17177000	26999	OsKitaake02g173200
Deletion	Chr1	31371325	31371327	2
Deletion	Chr2	36708417	36708418	1

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr5	6706720	7532318
Inversion	Chr10	6810773	7092328
Inversion	Chr10	6810775	7092335
Inversion	Chr7	9913989	10086012	2
Inversion	Chr7	9913997	10086015	2
Inversion	Chr11	10607706	10724448
Inversion	Chr11	10607720	10724459
Inversion	Chr8	27990801	28086616	OsKitaake08g236100
Inversion	Chr8	27990803	28086614	OsKitaake08g236100

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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