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Mutant Information

Mutant Name	FN1403-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN1403-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: 27

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 9327144 T-C Hetero SYNONYMOUS_CODING
SBS Chr1 10868302 C-T Homo INTERGENIC
SBS Chr1 40192323 A-C Hetero INTERGENIC
SBS Chr1 43524012 G-A Homo INTRON
SBS Chr3 15720279 T-A Hetero INTERGENIC
SBS Chr3 24169620 G-T Hetero INTERGENIC
SBS Chr3 28779969 T-C Hetero INTERGENIC
SBS Chr3 36843172 G-T Hetero UTR_3_PRIME
SBS Chr5 5059844 C-T Homo INTERGENIC
SBS Chr5 7459357 A-G Homo INTERGENIC
SBS Chr5 18328439 G-T Homo INTERGENIC
SBS Chr6 23778787 C-T Homo SYNONYMOUS_CODING
SBS Chr7 15120893 C-T Hetero INTERGENIC
SBS Chr7 15406933 A-T Homo INTERGENIC
SBS Chr7 20113859 C-T Hetero INTERGENIC
SBS Chr7 28154045 G-A Hetero INTERGENIC
SBS Chr8 7738229 T-C Homo INTERGENIC
SBS Chr8 11600415 G-A Homo INTERGENIC
SBS Chr9 7051773 C-T Homo INTERGENIC
SBS Chr9 9694334 T-A Homo STOP_GAINED OsKitaake09g058900
SBS Chr9 9694337 G-A Homo NON_SYNONYMOUS_CODING OsKitaake09g058900
SBS Chr10 1963501 G-A Homo INTERGENIC
SBS Chr10 5452037 G-T Hetero INTERGENIC
SBS Chr10 18484146 C-T Homo INTERGENIC
SBS Chr11 3792401 G-A Homo NON_SYNONYMOUS_CODING OsKitaake11g052700
SBS Chr12 12324666 G-A Homo INTERGENIC
SBS Chr12 16239942 G-A Hetero INTERGENIC

Deletions: 16

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr7 3604001 3613000 8999 OsKitaake07g046000
Deletion Chr9 9697656 9697657 1
Deletion Chr9 14872710 14872711 1
Deletion Chr2 16080001 16089000 8999 OsKitaake02g166300
Deletion Chr9 17379605 17379607 2
Deletion Chr10 18369276 18369292 16
Deletion Chr7 19285756 19285758 2
Deletion Chr9 19476784 19476800 16
Deletion Chr3 20075001 20209000 133999 3
Deletion Chr1 23254001 23273000 18999 OsKitaake01g222400
Deletion Chr12 25991045 25991046 1
Deletion Chr12 26177001 26207000 29999 4
Deletion Chr5 30208052 30208406 354
Deletion Chr1 31120334 31120349 15
Deletion Chr1 39901459 39901460 1
Deletion Chr1 42699001 42712000 12999

Insertions: 5

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr1 17625048 17625051 2
Insertion Chr1 26005535 26005538 2
Insertion Chr5 29401543 29401547 3
Insertion Chr11 23369788 23369791 2
Insertion Chr8 8067714 8067716 1

Inversions: 10

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Inversion Chr11 316333 1106881 OsKitaake11g013432
Inversion Chr3 1828893 2099115 OsKitaake03g026100
Inversion Chr3 1829049 2099122 OsKitaake03g026100
Inversion Chr9 9969409 10039166
Inversion Chr9 10039170 10040260
Inversion Chr3 22627764 22644703
Inversion Chr3 23577763 24158632
Inversion Chr3 23577881 24158641
Inversion Chr1 42621307 43064919 OsKitaake01g469400
Inversion Chr1 42623428 43065014 OsKitaake01g469500

Translocations: 6

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes

Translocation Chr3 1828912 Chr1 42623428 2
Translocation Chr3 1829046 Chr1 43065014 OsKitaake03g026100
Translocation Chr9 9969447 Chr2 15120170
Translocation Chr9 9973951 Chr2 15120160
Translocation Chr12 13193066 Chr1 43065108
Translocation Chr12 13193236 Chr1 42623519 OsKitaake01g469500

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	9327144	T-C	Hetero	SYNONYMOUS_CODING
SBS	Chr1	10868302	C-T	Homo	INTERGENIC
SBS	Chr1	40192323	A-C	Hetero	INTERGENIC
SBS	Chr1	43524012	G-A	Homo	INTRON
SBS	Chr3	15720279	T-A	Hetero	INTERGENIC
SBS	Chr3	24169620	G-T	Hetero	INTERGENIC
SBS	Chr3	28779969	T-C	Hetero	INTERGENIC
SBS	Chr3	36843172	G-T	Hetero	UTR_3_PRIME
SBS	Chr5	5059844	C-T	Homo	INTERGENIC
SBS	Chr5	7459357	A-G	Homo	INTERGENIC
SBS	Chr5	18328439	G-T	Homo	INTERGENIC
SBS	Chr6	23778787	C-T	Homo	SYNONYMOUS_CODING
SBS	Chr7	15120893	C-T	Hetero	INTERGENIC
SBS	Chr7	15406933	A-T	Homo	INTERGENIC
SBS	Chr7	20113859	C-T	Hetero	INTERGENIC
SBS	Chr7	28154045	G-A	Hetero	INTERGENIC
SBS	Chr8	7738229	T-C	Homo	INTERGENIC
SBS	Chr8	11600415	G-A	Homo	INTERGENIC
SBS	Chr9	7051773	C-T	Homo	INTERGENIC
SBS	Chr9	9694334	T-A	Homo	STOP_GAINED	OsKitaake09g058900
SBS	Chr9	9694337	G-A	Homo	NON_SYNONYMOUS_CODING	OsKitaake09g058900
SBS	Chr10	1963501	G-A	Homo	INTERGENIC
SBS	Chr10	5452037	G-T	Hetero	INTERGENIC
SBS	Chr10	18484146	C-T	Homo	INTERGENIC
SBS	Chr11	3792401	G-A	Homo	NON_SYNONYMOUS_CODING	OsKitaake11g052700
SBS	Chr12	12324666	G-A	Homo	INTERGENIC
SBS	Chr12	16239942	G-A	Hetero	INTERGENIC

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr7	3604001	3613000	8999	OsKitaake07g046000
Deletion	Chr9	9697656	9697657	1
Deletion	Chr9	14872710	14872711	1
Deletion	Chr2	16080001	16089000	8999	OsKitaake02g166300
Deletion	Chr9	17379605	17379607	2
Deletion	Chr10	18369276	18369292	16
Deletion	Chr7	19285756	19285758	2
Deletion	Chr9	19476784	19476800	16
Deletion	Chr3	20075001	20209000	133999	3
Deletion	Chr1	23254001	23273000	18999	OsKitaake01g222400
Deletion	Chr12	25991045	25991046	1
Deletion	Chr12	26177001	26207000	29999	4
Deletion	Chr5	30208052	30208406	354
Deletion	Chr1	31120334	31120349	15
Deletion	Chr1	39901459	39901460	1
Deletion	Chr1	42699001	42712000	12999

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr11	316333	1106881	OsKitaake11g013432
Inversion	Chr3	1828893	2099115	OsKitaake03g026100
Inversion	Chr3	1829049	2099122	OsKitaake03g026100
Inversion	Chr9	9969409	10039166
Inversion	Chr9	10039170	10040260
Inversion	Chr3	22627764	22644703
Inversion	Chr3	23577763	24158632
Inversion	Chr3	23577881	24158641
Inversion	Chr1	42621307	43064919	OsKitaake01g469400
Inversion	Chr1	42623428	43065014	OsKitaake01g469500

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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