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Mutant Information

Mutant Name	FN1236-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN1236-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) = Low (Between 25% and 74%) TO:0000430 (Germination Rate) = Normal (Between 75% and 125%) For more information, please see this phenotype file

Variant Information

Single base substitutions: 35

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 13628951 A-G Homo INTERGENIC
SBS Chr1 31017743 T-C Hetero INTERGENIC
SBS Chr1 31017762 G-A Hetero INTERGENIC
SBS Chr2 20667534 C-T Hetero INTERGENIC
SBS Chr2 25939010 T-C Homo SYNONYMOUS_CODING
SBS Chr2 27796232 A-C Homo SYNONYMOUS_CODING
SBS Chr2 33948755 A-G Homo INTERGENIC
SBS Chr3 29589340 T-C Hetero INTERGENIC
SBS Chr4 5680771 A-T Hetero INTERGENIC
SBS Chr4 5921476 T-C Hetero INTERGENIC
SBS Chr4 10661482 C-T Hetero INTERGENIC
SBS Chr4 15872035 T-A Hetero INTERGENIC
SBS Chr4 20871596 T-C Hetero NON_SYNONYMOUS_CODING OsKitaake04g113800
SBS Chr4 27168822 C-A Homo INTERGENIC
SBS Chr5 1931293 A-G Hetero INTERGENIC
SBS Chr5 24320323 G-T Homo STOP_GAINED OsKitaake05g217300
SBS Chr5 24382658 A-G Homo INTERGENIC
SBS Chr6 4176453 A-T Hetero INTERGENIC
SBS Chr7 3996723 T-G Hetero SYNONYMOUS_CODING
SBS Chr7 5878257 C-T Hetero INTERGENIC
SBS Chr7 11065943 G-A Homo INTERGENIC
SBS Chr7 27693922 T-C Hetero INTERGENIC
SBS Chr8 3213413 C-T Hetero INTERGENIC
SBS Chr8 15955763 T-C Hetero INTERGENIC
SBS Chr9 2695030 T-C Hetero INTERGENIC
SBS Chr9 15062984 A-T Hetero INTERGENIC
SBS Chr10 2709838 G-T Hetero INTERGENIC
SBS Chr10 9100375 C-T Homo INTERGENIC
SBS Chr10 9766031 G-A Hetero INTERGENIC
SBS Chr10 11713055 A-T Hetero INTRON
SBS Chr10 12892768 C-G Hetero INTERGENIC
SBS Chr11 13928461 C-T Hetero INTERGENIC
SBS Chr11 16295728 A-C Hetero INTERGENIC
SBS Chr12 2654527 T-G Hetero INTERGENIC
SBS Chr12 9580495 A-T Homo INTERGENIC

Deletions: 16

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr2 7630001 7710000 79999 7
Deletion Chr6 7655832 7655836 4
Deletion Chr10 9983862 9983863 1
Deletion Chr1 10183405 10183413 8
Deletion Chr6 10682001 10775000 92999 12
Deletion Chr12 11750843 11750848 5
Deletion Chr9 12451817 12451826 9
Deletion Chr8 12807026 12807027 1
Deletion Chr8 13701739 13701740 1
Deletion Chr8 14190925 14190933 8
Deletion Chr10 15468957 15468959 2
Deletion Chr9 16118470 16118472 2
Deletion Chr9 16912451 16912520 69
Deletion Chr4 26077495 26077501 6
Deletion Chr8 27506311 27506320 9
Deletion Chr5 30223346 30223347 1

Insertions: 2

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr1 43985976 43985979 2
Insertion Chr1 44064508 44064511 2

Inversions: 6

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Inversion Chr3 8801312 8853285 2
Inversion Chr3 8801316 8853302 2
Inversion Chr12 10484725 10994042
Inversion Chr6 10681711 10800393 2
Inversion Chr6 10797764 10800416 2
Inversion Chr6 12137424 12203504

Translocations: 1

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes

Translocation Chr5 13959176 Chr2 27441667 OsKitaake02g275700

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	13628951	A-G	Homo	INTERGENIC
SBS	Chr1	31017743	T-C	Hetero	INTERGENIC
SBS	Chr1	31017762	G-A	Hetero	INTERGENIC
SBS	Chr2	20667534	C-T	Hetero	INTERGENIC
SBS	Chr2	25939010	T-C	Homo	SYNONYMOUS_CODING
SBS	Chr2	27796232	A-C	Homo	SYNONYMOUS_CODING
SBS	Chr2	33948755	A-G	Homo	INTERGENIC
SBS	Chr3	29589340	T-C	Hetero	INTERGENIC
SBS	Chr4	5680771	A-T	Hetero	INTERGENIC
SBS	Chr4	5921476	T-C	Hetero	INTERGENIC
SBS	Chr4	10661482	C-T	Hetero	INTERGENIC
SBS	Chr4	15872035	T-A	Hetero	INTERGENIC
SBS	Chr4	20871596	T-C	Hetero	NON_SYNONYMOUS_CODING	OsKitaake04g113800
SBS	Chr4	27168822	C-A	Homo	INTERGENIC
SBS	Chr5	1931293	A-G	Hetero	INTERGENIC
SBS	Chr5	24320323	G-T	Homo	STOP_GAINED	OsKitaake05g217300
SBS	Chr5	24382658	A-G	Homo	INTERGENIC
SBS	Chr6	4176453	A-T	Hetero	INTERGENIC
SBS	Chr7	3996723	T-G	Hetero	SYNONYMOUS_CODING
SBS	Chr7	5878257	C-T	Hetero	INTERGENIC
SBS	Chr7	11065943	G-A	Homo	INTERGENIC
SBS	Chr7	27693922	T-C	Hetero	INTERGENIC
SBS	Chr8	3213413	C-T	Hetero	INTERGENIC
SBS	Chr8	15955763	T-C	Hetero	INTERGENIC
SBS	Chr9	2695030	T-C	Hetero	INTERGENIC
SBS	Chr9	15062984	A-T	Hetero	INTERGENIC
SBS	Chr10	2709838	G-T	Hetero	INTERGENIC
SBS	Chr10	9100375	C-T	Homo	INTERGENIC
SBS	Chr10	9766031	G-A	Hetero	INTERGENIC
SBS	Chr10	11713055	A-T	Hetero	INTRON
SBS	Chr10	12892768	C-G	Hetero	INTERGENIC
SBS	Chr11	13928461	C-T	Hetero	INTERGENIC
SBS	Chr11	16295728	A-C	Hetero	INTERGENIC
SBS	Chr12	2654527	T-G	Hetero	INTERGENIC
SBS	Chr12	9580495	A-T	Homo	INTERGENIC

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr2	7630001	7710000	79999	7
Deletion	Chr6	7655832	7655836	4
Deletion	Chr10	9983862	9983863	1
Deletion	Chr1	10183405	10183413	8
Deletion	Chr6	10682001	10775000	92999	12
Deletion	Chr12	11750843	11750848	5
Deletion	Chr9	12451817	12451826	9
Deletion	Chr8	12807026	12807027	1
Deletion	Chr8	13701739	13701740	1
Deletion	Chr8	14190925	14190933	8
Deletion	Chr10	15468957	15468959	2
Deletion	Chr9	16118470	16118472	2
Deletion	Chr9	16912451	16912520	69
Deletion	Chr4	26077495	26077501	6
Deletion	Chr8	27506311	27506320	9
Deletion	Chr5	30223346	30223347	1

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr3	8801312	8853285	2
Inversion	Chr3	8801316	8853302	2
Inversion	Chr12	10484725	10994042
Inversion	Chr6	10681711	10800393	2
Inversion	Chr6	10797764	10800416	2
Inversion	Chr6	12137424	12203504

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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