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Mutant Information

Mutant Name	FN1396-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN1396-S Alignment File
Seed Availability	Yes [Order Seeds]
Phenotype	TO:0000326 (Leaf Color) = Normal TO:0000137 (Days to heading) = Normal (Between 75% and 125%) TO:0000346 (Tiller number) = Normal (Between 75% and 125%) TO:0000430 (Germination Rate) = 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 Chr2 6446290 A-G Hetero INTERGENIC
SBS Chr2 10219188 C-G Homo INTRON
SBS Chr2 17132862 A-G Homo INTERGENIC
SBS Chr3 4563857 C-A Hetero UTR_3_PRIME
SBS Chr3 7306189 C-T Homo INTRON
SBS Chr3 11886560 G-T Homo INTERGENIC
SBS Chr3 14637200 C-T Homo INTERGENIC
SBS Chr3 33112431 T-A Hetero INTERGENIC
SBS Chr4 13605934 A-G Homo INTERGENIC
SBS Chr4 28094980 T-A Homo INTERGENIC
SBS Chr4 28094981 T-A Homo INTERGENIC
SBS Chr4 28129491 G-A Homo INTERGENIC
SBS Chr5 2219375 A-G Homo UTR_3_PRIME
SBS Chr5 13514085 T-A Hetero INTERGENIC
SBS Chr5 24569638 C-A Homo INTERGENIC
SBS Chr5 24986238 A-G Hetero INTERGENIC
SBS Chr5 27029542 G-A Homo INTERGENIC
SBS Chr6 23724713 A-G Hetero INTERGENIC
SBS Chr6 28415121 T-A Hetero INTRON
SBS Chr8 1523321 C-T Homo NON_SYNONYMOUS_CODING OsKitaake08g019000
SBS Chr9 3054606 T-C Hetero INTERGENIC
SBS Chr9 5766202 G-A Hetero INTERGENIC
SBS Chr10 5152601 T-C Homo INTERGENIC
SBS Chr10 9517501 C-A Hetero INTERGENIC
SBS Chr10 16277114 A-G Hetero INTERGENIC
SBS Chr10 22061873 A-T Homo INTERGENIC
SBS Chr11 24807073 T-A Homo INTERGENIC
SBS Chr12 22491985 C-T Hetero INTERGENIC
SBS Chr12 22718613 G-A Homo UTR_5_PRIME
SBS Chr12 22718619 C-A Homo START_GAINED

Deletions: 15

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr7 11692014 11692015 1
Deletion Chr3 11854649 11854676 27 OsKitaake03g161400
Deletion Chr7 12264001 12280000 15999
Deletion Chr7 13721001 13727000 5999
Deletion Chr7 15809268 15809270 2
Deletion Chr7 15922632 15922633 1
Deletion Chr6 18099415 18099541 126
Deletion Chr3 19445209 19445210 1
Deletion Chr3 23767100 23767102 2
Deletion Chr4 26025923 26025931 8
Deletion Chr1 31725166 31725167 1
Deletion Chr4 32064010 32064011 1
Deletion Chr1 38775368 38775381 13 OsKitaake01g415100
Deletion Chr1 39862188 39862298 110
Deletion Chr1 40000743 40000748 5 OsKitaake01g433200

Insertions: 4

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr8 27321247 27321250 2
Insertion Chr9 7344810 7344813 2
Insertion Chr4 10335753 10335755 1
Insertion Chr6 11349 11351 1

Inversions: 4

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Inversion Chr8 11188377 12115676 OsKitaake08g105600
Inversion Chr8 11188398 12115678 OsKitaake08g105600
Inversion Chr7 13357227 14001783 OsKitaake07g117900
Inversion Chr7 14001786 14134808

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr2	6446290	A-G	Hetero	INTERGENIC
SBS	Chr2	10219188	C-G	Homo	INTRON
SBS	Chr2	17132862	A-G	Homo	INTERGENIC
SBS	Chr3	4563857	C-A	Hetero	UTR_3_PRIME
SBS	Chr3	7306189	C-T	Homo	INTRON
SBS	Chr3	11886560	G-T	Homo	INTERGENIC
SBS	Chr3	14637200	C-T	Homo	INTERGENIC
SBS	Chr3	33112431	T-A	Hetero	INTERGENIC
SBS	Chr4	13605934	A-G	Homo	INTERGENIC
SBS	Chr4	28094980	T-A	Homo	INTERGENIC
SBS	Chr4	28094981	T-A	Homo	INTERGENIC
SBS	Chr4	28129491	G-A	Homo	INTERGENIC
SBS	Chr5	2219375	A-G	Homo	UTR_3_PRIME
SBS	Chr5	13514085	T-A	Hetero	INTERGENIC
SBS	Chr5	24569638	C-A	Homo	INTERGENIC
SBS	Chr5	24986238	A-G	Hetero	INTERGENIC
SBS	Chr5	27029542	G-A	Homo	INTERGENIC
SBS	Chr6	23724713	A-G	Hetero	INTERGENIC
SBS	Chr6	28415121	T-A	Hetero	INTRON
SBS	Chr8	1523321	C-T	Homo	NON_SYNONYMOUS_CODING	OsKitaake08g019000
SBS	Chr9	3054606	T-C	Hetero	INTERGENIC
SBS	Chr9	5766202	G-A	Hetero	INTERGENIC
SBS	Chr10	5152601	T-C	Homo	INTERGENIC
SBS	Chr10	9517501	C-A	Hetero	INTERGENIC
SBS	Chr10	16277114	A-G	Hetero	INTERGENIC
SBS	Chr10	22061873	A-T	Homo	INTERGENIC
SBS	Chr11	24807073	T-A	Homo	INTERGENIC
SBS	Chr12	22491985	C-T	Hetero	INTERGENIC
SBS	Chr12	22718613	G-A	Homo	UTR_5_PRIME
SBS	Chr12	22718619	C-A	Homo	START_GAINED

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr7	11692014	11692015	1
Deletion	Chr3	11854649	11854676	27	OsKitaake03g161400
Deletion	Chr7	12264001	12280000	15999
Deletion	Chr7	13721001	13727000	5999
Deletion	Chr7	15809268	15809270	2
Deletion	Chr7	15922632	15922633	1
Deletion	Chr6	18099415	18099541	126
Deletion	Chr3	19445209	19445210	1
Deletion	Chr3	23767100	23767102	2
Deletion	Chr4	26025923	26025931	8
Deletion	Chr1	31725166	31725167	1
Deletion	Chr4	32064010	32064011	1
Deletion	Chr1	38775368	38775381	13	OsKitaake01g415100
Deletion	Chr1	39862188	39862298	110
Deletion	Chr1	40000743	40000748	5	OsKitaake01g433200

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr8	11188377	12115676	OsKitaake08g105600
Inversion	Chr8	11188398	12115678	OsKitaake08g105600
Inversion	Chr7	13357227	14001783	OsKitaake07g117900
Inversion	Chr7	14001786	14134808

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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