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Mutant Information

Mutant Name	FN1559-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN1559-S Alignment File
Seed Availability	Yes [Order Seeds]
Phenotype	TO:0000326 (Leaf Color) = Normal 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: 40

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 6482098 C-T Homo INTRON
SBS Chr1 6482099 A-C Homo INTRON
SBS Chr1 10210585 T-C Hetero INTERGENIC
SBS Chr1 13894633 A-T Hetero INTERGENIC
SBS Chr1 16902955 T-C Hetero INTERGENIC
SBS Chr1 17973840 G-A Hetero INTERGENIC
SBS Chr1 17973851 G-A Hetero INTERGENIC
SBS Chr1 24981567 G-A Hetero INTERGENIC
SBS Chr1 33644063 C-T Homo NON_SYNONYMOUS_CODING OsKitaake01g344800
SBS Chr2 1602903 G-A Hetero INTERGENIC
SBS Chr2 27022244 T-G Homo INTERGENIC
SBS Chr2 30535600 T-C Hetero UTR_3_PRIME
SBS Chr3 15618232 G-C Hetero NON_SYNONYMOUS_CODING OsKitaake03g200600
SBS Chr3 19302246 C-A Hetero INTERGENIC
SBS Chr3 19690178 C-G Hetero INTERGENIC
SBS Chr3 20950884 G-T Hetero INTERGENIC
SBS Chr3 30125034 C-T Hetero INTERGENIC
SBS Chr4 4550704 A-C Homo INTERGENIC
SBS Chr4 17172413 T-C Homo INTERGENIC
SBS Chr4 18662962 C-A Hetero INTERGENIC
SBS Chr4 24852057 G-T Homo INTERGENIC
SBS Chr4 34269744 A-C Hetero UTR_3_PRIME
SBS Chr5 9029861 C-T Hetero INTERGENIC
SBS Chr5 11314324 G-C Hetero INTERGENIC
SBS Chr6 973442 A-G Homo INTERGENIC
SBS Chr6 4389859 G-A Homo UTR_5_PRIME
SBS Chr6 10474604 G-C Homo INTRON
SBS Chr6 14297624 C-A Homo INTERGENIC
SBS Chr7 18924593 T-C Homo INTERGENIC
SBS Chr7 19037345 C-T Homo INTERGENIC
SBS Chr7 25610901 C-A Homo UTR_5_PRIME
SBS Chr8 2723631 G-A Homo INTERGENIC
SBS Chr8 9023869 C-T Homo INTERGENIC
SBS Chr9 10054378 G-T Hetero INTERGENIC
SBS Chr10 32278 G-A Homo INTERGENIC
SBS Chr10 3965620 T-A Hetero INTERGENIC
SBS Chr10 10173279 A-G Hetero INTERGENIC
SBS Chr10 16162500 C-G Homo NON_SYNONYMOUS_CODING OsKitaake10g108300
SBS Chr11 19185658 G-A Hetero INTERGENIC
SBS Chr12 16852184 A-C Hetero INTERGENIC

Deletions: 15

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr1 4658673 4658684 11
Deletion Chr7 6742474 6742477 3
Deletion Chr6 9161727 9161728 1
Deletion Chr2 9539589 9539591 2
Deletion Chr9 10696001 10707000 10999 OsKitaake09g066600
Deletion Chr7 11568311 11568313 2
Deletion Chr11 12075031 12075036 5
Deletion Chr8 12807026 12807027 1
Deletion Chr1 13684134 13684135 1
Deletion Chr11 17717882 17718008 126
Deletion Chr4 18828001 18859000 30999 OsKitaake04g094600
Deletion Chr2 21376043 21376044 1
Deletion Chr4 24391839 24391935 96 OsKitaake04g158400
Deletion Chr1 26588174 26588175 1
Deletion Chr1 39990362 39990376 14

Insertions: 5

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr5 10605087 10605093 5
Insertion Chr12 4052293 4052296 2
Insertion Chr7 11037064 11037069 4
Insertion Chr8 22823116 22823118 1
Insertion Chr8 22826309 22826311 1

Inversions: 6

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Inversion Chr12 3070239 3283912 OsKitaake12g044800
Inversion Chr12 3070240 3283904 OsKitaake12g044800
Inversion Chr6 13694930 14120539 OsKitaake06g143401
Inversion Chr6 13694931 14120542 OsKitaake06g143401
Inversion Chr4 18827838 18990499 OsKitaake04g094600
Inversion Chr4 18986430 18990512

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	6482098	C-T	Homo	INTRON
SBS	Chr1	6482099	A-C	Homo	INTRON
SBS	Chr1	10210585	T-C	Hetero	INTERGENIC
SBS	Chr1	13894633	A-T	Hetero	INTERGENIC
SBS	Chr1	16902955	T-C	Hetero	INTERGENIC
SBS	Chr1	17973840	G-A	Hetero	INTERGENIC
SBS	Chr1	17973851	G-A	Hetero	INTERGENIC
SBS	Chr1	24981567	G-A	Hetero	INTERGENIC
SBS	Chr1	33644063	C-T	Homo	NON_SYNONYMOUS_CODING	OsKitaake01g344800
SBS	Chr2	1602903	G-A	Hetero	INTERGENIC
SBS	Chr2	27022244	T-G	Homo	INTERGENIC
SBS	Chr2	30535600	T-C	Hetero	UTR_3_PRIME
SBS	Chr3	15618232	G-C	Hetero	NON_SYNONYMOUS_CODING	OsKitaake03g200600
SBS	Chr3	19302246	C-A	Hetero	INTERGENIC
SBS	Chr3	19690178	C-G	Hetero	INTERGENIC
SBS	Chr3	20950884	G-T	Hetero	INTERGENIC
SBS	Chr3	30125034	C-T	Hetero	INTERGENIC
SBS	Chr4	4550704	A-C	Homo	INTERGENIC
SBS	Chr4	17172413	T-C	Homo	INTERGENIC
SBS	Chr4	18662962	C-A	Hetero	INTERGENIC
SBS	Chr4	24852057	G-T	Homo	INTERGENIC
SBS	Chr4	34269744	A-C	Hetero	UTR_3_PRIME
SBS	Chr5	9029861	C-T	Hetero	INTERGENIC
SBS	Chr5	11314324	G-C	Hetero	INTERGENIC
SBS	Chr6	973442	A-G	Homo	INTERGENIC
SBS	Chr6	4389859	G-A	Homo	UTR_5_PRIME
SBS	Chr6	10474604	G-C	Homo	INTRON
SBS	Chr6	14297624	C-A	Homo	INTERGENIC
SBS	Chr7	18924593	T-C	Homo	INTERGENIC
SBS	Chr7	19037345	C-T	Homo	INTERGENIC
SBS	Chr7	25610901	C-A	Homo	UTR_5_PRIME
SBS	Chr8	2723631	G-A	Homo	INTERGENIC
SBS	Chr8	9023869	C-T	Homo	INTERGENIC
SBS	Chr9	10054378	G-T	Hetero	INTERGENIC
SBS	Chr10	32278	G-A	Homo	INTERGENIC
SBS	Chr10	3965620	T-A	Hetero	INTERGENIC
SBS	Chr10	10173279	A-G	Hetero	INTERGENIC
SBS	Chr10	16162500	C-G	Homo	NON_SYNONYMOUS_CODING	OsKitaake10g108300
SBS	Chr11	19185658	G-A	Hetero	INTERGENIC
SBS	Chr12	16852184	A-C	Hetero	INTERGENIC

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr1	4658673	4658684	11
Deletion	Chr7	6742474	6742477	3
Deletion	Chr6	9161727	9161728	1
Deletion	Chr2	9539589	9539591	2
Deletion	Chr9	10696001	10707000	10999	OsKitaake09g066600
Deletion	Chr7	11568311	11568313	2
Deletion	Chr11	12075031	12075036	5
Deletion	Chr8	12807026	12807027	1
Deletion	Chr1	13684134	13684135	1
Deletion	Chr11	17717882	17718008	126
Deletion	Chr4	18828001	18859000	30999	OsKitaake04g094600
Deletion	Chr2	21376043	21376044	1
Deletion	Chr4	24391839	24391935	96	OsKitaake04g158400
Deletion	Chr1	26588174	26588175	1
Deletion	Chr1	39990362	39990376	14

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr12	3070239	3283912	OsKitaake12g044800
Inversion	Chr12	3070240	3283904	OsKitaake12g044800
Inversion	Chr6	13694930	14120539	OsKitaake06g143401
Inversion	Chr6	13694931	14120542	OsKitaake06g143401
Inversion	Chr4	18827838	18990499	OsKitaake04g094600
Inversion	Chr4	18986430	18990512

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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