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Mutant Information

Mutant Name	FN403-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN403-S Alignment File
Seed Availability	Yes [Order Seeds]
Phenotype	TO:0000430 (Germination Rate) = Low (Between 25% and 75%) For more information, please see this phenotype file

Variant Information

Single base substitutions: 28

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 13519699 T-A Homo INTERGENIC
SBS Chr1 25571644 G-A Hetero INTERGENIC
SBS Chr1 26939243 A-G Hetero INTERGENIC
SBS Chr1 35422503 A-T Hetero NON_SYNONYMOUS_CODING OsKitaake01g373600
SBS Chr2 10219892 G-A Hetero INTRON
SBS Chr2 22869513 A-G Hetero INTERGENIC
SBS Chr3 5038834 G-A Hetero INTERGENIC
SBS Chr3 11405971 C-T Hetero INTERGENIC
SBS Chr3 14106186 T-C Hetero INTRON
SBS Chr3 28299626 G-A Homo INTERGENIC
SBS Chr3 36489061 A-G Homo UTR_5_PRIME
SBS Chr4 7657048 T-C Hetero NON_SYNONYMOUS_CODING OsKitaake04g038500
SBS Chr4 10689174 T-C Hetero INTERGENIC
SBS Chr4 20662665 G-A Hetero INTERGENIC
SBS Chr5 7997107 G-A Hetero INTERGENIC
SBS Chr5 11146388 A-G Hetero INTERGENIC
SBS Chr5 11459192 G-A Hetero INTERGENIC
SBS Chr5 28388380 G-C Hetero SYNONYMOUS_CODING
SBS Chr8 298524 G-A Hetero INTERGENIC
SBS Chr8 4412020 C-T Hetero INTERGENIC
SBS Chr9 19714893 T-A Hetero INTRON
SBS Chr9 21741791 C-T Hetero INTRON
SBS Chr10 20122041 T-C Hetero INTERGENIC
SBS Chr11 7774795 G-T Hetero INTRON
SBS Chr11 14477488 G-A Hetero INTERGENIC
SBS Chr11 17150793 C-T Homo INTERGENIC
SBS Chr11 19458409 A-T Hetero INTERGENIC
SBS Chr12 12650029 C-T Hetero INTERGENIC

Deletions: 11

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr5 2526375 2526380 5
Deletion Chr5 3509849 3509866 17
Deletion Chr11 7187001 7215000 27999 5
Deletion Chr1 9103612 9103620 8
Deletion Chr9 10008132 10008134 2
Deletion Chr11 11969933 11969943 10 OsKitaake11g110900
Deletion Chr11 13716517 13716523 6
Deletion Chr11 15005257 15005260 3
Deletion Chr6 19094960 19094961 1
Deletion Chr4 36146486 36146489 3
Deletion Chr3 36494267 36494272 5

Insertions: 5

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr4 36805150 36805153 2
Insertion Chr10 19277237 19277240 2
Insertion Chr12 10016519 10016522 2
Insertion Chr5 30126816 30126818 1
Insertion Chr5 30232136 30232144 7

Inversions: 4

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Inversion Chr1 7326808 7617095 OsKitaake01g091900
Inversion Chr1 7326835 7617095 OsKitaake01g091900
Inversion Chr9 13662681 13665233
Inversion Chr9 13662710 13665250

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	13519699	T-A	Homo	INTERGENIC
SBS	Chr1	25571644	G-A	Hetero	INTERGENIC
SBS	Chr1	26939243	A-G	Hetero	INTERGENIC
SBS	Chr1	35422503	A-T	Hetero	NON_SYNONYMOUS_CODING	OsKitaake01g373600
SBS	Chr2	10219892	G-A	Hetero	INTRON
SBS	Chr2	22869513	A-G	Hetero	INTERGENIC
SBS	Chr3	5038834	G-A	Hetero	INTERGENIC
SBS	Chr3	11405971	C-T	Hetero	INTERGENIC
SBS	Chr3	14106186	T-C	Hetero	INTRON
SBS	Chr3	28299626	G-A	Homo	INTERGENIC
SBS	Chr3	36489061	A-G	Homo	UTR_5_PRIME
SBS	Chr4	7657048	T-C	Hetero	NON_SYNONYMOUS_CODING	OsKitaake04g038500
SBS	Chr4	10689174	T-C	Hetero	INTERGENIC
SBS	Chr4	20662665	G-A	Hetero	INTERGENIC
SBS	Chr5	7997107	G-A	Hetero	INTERGENIC
SBS	Chr5	11146388	A-G	Hetero	INTERGENIC
SBS	Chr5	11459192	G-A	Hetero	INTERGENIC
SBS	Chr5	28388380	G-C	Hetero	SYNONYMOUS_CODING
SBS	Chr8	298524	G-A	Hetero	INTERGENIC
SBS	Chr8	4412020	C-T	Hetero	INTERGENIC
SBS	Chr9	19714893	T-A	Hetero	INTRON
SBS	Chr9	21741791	C-T	Hetero	INTRON
SBS	Chr10	20122041	T-C	Hetero	INTERGENIC
SBS	Chr11	7774795	G-T	Hetero	INTRON
SBS	Chr11	14477488	G-A	Hetero	INTERGENIC
SBS	Chr11	17150793	C-T	Homo	INTERGENIC
SBS	Chr11	19458409	A-T	Hetero	INTERGENIC
SBS	Chr12	12650029	C-T	Hetero	INTERGENIC

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr5	2526375	2526380	5
Deletion	Chr5	3509849	3509866	17
Deletion	Chr11	7187001	7215000	27999	5
Deletion	Chr1	9103612	9103620	8
Deletion	Chr9	10008132	10008134	2
Deletion	Chr11	11969933	11969943	10	OsKitaake11g110900
Deletion	Chr11	13716517	13716523	6
Deletion	Chr11	15005257	15005260	3
Deletion	Chr6	19094960	19094961	1
Deletion	Chr4	36146486	36146489	3
Deletion	Chr3	36494267	36494272	5

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr1	7326808	7617095	OsKitaake01g091900
Inversion	Chr1	7326835	7617095	OsKitaake01g091900
Inversion	Chr9	13662681	13665233
Inversion	Chr9	13662710	13665250

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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