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Mutant Information

Mutant Name	FN1249-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN1249-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: 24

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 23340340 T-C Homo INTERGENIC
SBS Chr3 22714350 C-T Hetero INTERGENIC
SBS Chr3 27963973 T-G Hetero INTERGENIC
SBS Chr3 32018804 A-G Hetero INTERGENIC
SBS Chr4 1617976 G-A Hetero INTRON
SBS Chr4 12181549 G-T Hetero INTERGENIC
SBS Chr4 12181552 G-T Hetero INTERGENIC
SBS Chr4 17514397 A-T Hetero INTERGENIC
SBS Chr4 20741363 A-G Hetero INTERGENIC
SBS Chr5 11757796 T-C Hetero INTERGENIC
SBS Chr6 2755711 G-T Homo INTERGENIC
SBS Chr6 5319453 G-C Homo SYNONYMOUS_CODING
SBS Chr6 24715564 G-A Hetero INTERGENIC
SBS Chr6 24715566 C-T Hetero INTERGENIC
SBS Chr8 20413750 C-T Hetero INTERGENIC
SBS Chr9 1701481 G-A Hetero INTERGENIC
SBS Chr9 10285574 G-C Hetero INTRON
SBS Chr10 12520540 T-A Hetero INTERGENIC
SBS Chr11 4548871 T-C Hetero INTRON
SBS Chr11 16319949 C-T Hetero INTERGENIC
SBS Chr11 20370067 C-T Hetero INTERGENIC
SBS Chr11 27931620 G-C Hetero UTR_5_PRIME
SBS Chr12 5223984 C-T Homo INTERGENIC
SBS Chr12 7083887 A-G Homo INTERGENIC

Deletions: 17

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr1 1797294 1797297 3
Deletion Chr9 6686003 6686105 102
Deletion Chr7 8464411 8464484 73
Deletion Chr6 9586001 9750000 163999 10
Deletion Chr5 10345261 10345274 13
Deletion Chr5 10613953 10613954 1
Deletion Chr4 12183406 12183410 4
Deletion Chr2 14625215 14625217 2
Deletion Chr12 21458282 21458287 5
Deletion Chr1 23974023 23974024 1
Deletion Chr7 25767780 25767792 12
Deletion Chr7 26281167 26281174 7
Deletion Chr8 26765464 26765465 1
Deletion Chr8 27706574 27706576 2
Deletion Chr2 28980926 28980931 5
Deletion Chr4 32776001 32964000 187999 25
Deletion Chr4 32967001 33077000 109999 14

Insertions: 3

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr7 28346703 28346707 3
Insertion Chr8 9161972 9161975 2
Insertion Chr9 18630496 18630499 2

Inversions: 2

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Inversion Chr4 32776405 33121743 OsKitaake04g264500
Inversion Chr4 33076600 33121752

Translocations: 2

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes

Translocation Chr6 22868302 Chr3 20378864 2
Translocation Chr6 22899052 Chr3 20378861 OsKitaake03g230800

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	23340340	T-C	Homo	INTERGENIC
SBS	Chr3	22714350	C-T	Hetero	INTERGENIC
SBS	Chr3	27963973	T-G	Hetero	INTERGENIC
SBS	Chr3	32018804	A-G	Hetero	INTERGENIC
SBS	Chr4	1617976	G-A	Hetero	INTRON
SBS	Chr4	12181549	G-T	Hetero	INTERGENIC
SBS	Chr4	12181552	G-T	Hetero	INTERGENIC
SBS	Chr4	17514397	A-T	Hetero	INTERGENIC
SBS	Chr4	20741363	A-G	Hetero	INTERGENIC
SBS	Chr5	11757796	T-C	Hetero	INTERGENIC
SBS	Chr6	2755711	G-T	Homo	INTERGENIC
SBS	Chr6	5319453	G-C	Homo	SYNONYMOUS_CODING
SBS	Chr6	24715564	G-A	Hetero	INTERGENIC
SBS	Chr6	24715566	C-T	Hetero	INTERGENIC
SBS	Chr8	20413750	C-T	Hetero	INTERGENIC
SBS	Chr9	1701481	G-A	Hetero	INTERGENIC
SBS	Chr9	10285574	G-C	Hetero	INTRON
SBS	Chr10	12520540	T-A	Hetero	INTERGENIC
SBS	Chr11	4548871	T-C	Hetero	INTRON
SBS	Chr11	16319949	C-T	Hetero	INTERGENIC
SBS	Chr11	20370067	C-T	Hetero	INTERGENIC
SBS	Chr11	27931620	G-C	Hetero	UTR_5_PRIME
SBS	Chr12	5223984	C-T	Homo	INTERGENIC
SBS	Chr12	7083887	A-G	Homo	INTERGENIC

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr1	1797294	1797297	3
Deletion	Chr9	6686003	6686105	102
Deletion	Chr7	8464411	8464484	73
Deletion	Chr6	9586001	9750000	163999	10
Deletion	Chr5	10345261	10345274	13
Deletion	Chr5	10613953	10613954	1
Deletion	Chr4	12183406	12183410	4
Deletion	Chr2	14625215	14625217	2
Deletion	Chr12	21458282	21458287	5
Deletion	Chr1	23974023	23974024	1
Deletion	Chr7	25767780	25767792	12
Deletion	Chr7	26281167	26281174	7
Deletion	Chr8	26765464	26765465	1
Deletion	Chr8	27706574	27706576	2
Deletion	Chr2	28980926	28980931	5
Deletion	Chr4	32776001	32964000	187999	25
Deletion	Chr4	32967001	33077000	109999	14

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr4	32776405	33121743	OsKitaake04g264500
Inversion	Chr4	33076600	33121752

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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