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Mutant Information

Mutant Name	FN553-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN553-S Alignment File
Seed Availability	Yes [Order Seeds]
Phenotype	TO:0000430 (Germination Rate) = Very Low (Below 24%) For more information, please see this phenotype file

Variant Information

Single base substitutions: 25

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 384202 A-T Hetero INTRON
SBS Chr1 5602585 A-T Homo STOP_GAINED OsKitaake01g071800
SBS Chr1 13062588 A-T Hetero INTERGENIC
SBS Chr1 38131415 C-T Hetero INTERGENIC
SBS Chr1 40526811 T-C Homo INTERGENIC
SBS Chr2 13212035 A-G Homo INTERGENIC
SBS Chr3 3151799 T-A Hetero INTERGENIC
SBS Chr3 6812276 A-G Hetero INTERGENIC
SBS Chr4 23156206 A-T Homo INTRON
SBS Chr4 25919681 G-A Hetero INTRON
SBS Chr4 25919683 G-A Hetero INTRON
SBS Chr5 21208091 T-C Hetero INTERGENIC
SBS Chr6 2161590 C-T Hetero INTERGENIC
SBS Chr7 27032998 T-A Hetero NON_SYNONYMOUS_CODING OsKitaake07g252700
SBS Chr7 29041315 G-T Hetero INTERGENIC
SBS Chr8 3427768 T-A Homo INTERGENIC
SBS Chr8 6112875 G-A Homo UTR_3_PRIME
SBS Chr8 25059665 G-T Homo INTRON
SBS Chr9 8764891 A-G Hetero INTERGENIC
SBS Chr9 10402616 C-T Hetero INTRON
SBS Chr10 21619695 C-A Hetero INTERGENIC
SBS Chr11 14901562 A-G Hetero INTERGENIC
SBS Chr11 18429560 G-T Hetero INTERGENIC
SBS Chr11 23911894 C-T Homo INTERGENIC
SBS Chr11 26261052 C-T Homo INTERGENIC

Deletions: 15

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr6 15859 15860 1
Deletion Chr11 2464612 2464613 1
Deletion Chr8 3564129 3564130 1
Deletion Chr11 4101816 4101824 8
Deletion Chr5 7910001 7940000 29999
Deletion Chr3 8497515 8497516 1
Deletion Chr12 12301219 12301232 13
Deletion Chr7 13701001 13726000 24999
Deletion Chr10 18868801 18868802 1
Deletion Chr10 20351563 20351566 3
Deletion Chr7 25343952 25343953 1 OsKitaake07g229500
Deletion Chr11 27496867 27496870 3
Deletion Chr2 28172837 28172840 3
Deletion Chr2 33419932 33419933 1
Deletion Chr1 40963857 40963867 10 OsKitaake01g446900

Insertions: 7

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr1 43431302 43431307 4
Insertion Chr2 35473911 35473914 2
Insertion Chr3 3508581 3508584 2
Insertion Chr3 16382955 16382958 2
Insertion Chr9 3057509 3057512 2
Insertion Chr10 12881865 12881868 2
Insertion Chr1 17222099 17222101 1

Inversions: 2

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Inversion Chr10 176353 942475
Inversion Chr10 176359 942488

Translocations: 5

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes

Translocation Chr8 251675 Chr5 6462278
Translocation Chr8 251942 Chr5 6462283
Translocation Chr5 20591323 Chr1 30549649 OsKitaake05g164100
Translocation Chr5 20592310 Chr1 30549613 OsKitaake05g164100
Translocation Chr8 21916146 Chr4 21123067 OsKitaake08g165800

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	384202	A-T	Hetero	INTRON
SBS	Chr1	5602585	A-T	Homo	STOP_GAINED	OsKitaake01g071800
SBS	Chr1	13062588	A-T	Hetero	INTERGENIC
SBS	Chr1	38131415	C-T	Hetero	INTERGENIC
SBS	Chr1	40526811	T-C	Homo	INTERGENIC
SBS	Chr2	13212035	A-G	Homo	INTERGENIC
SBS	Chr3	3151799	T-A	Hetero	INTERGENIC
SBS	Chr3	6812276	A-G	Hetero	INTERGENIC
SBS	Chr4	23156206	A-T	Homo	INTRON
SBS	Chr4	25919681	G-A	Hetero	INTRON
SBS	Chr4	25919683	G-A	Hetero	INTRON
SBS	Chr5	21208091	T-C	Hetero	INTERGENIC
SBS	Chr6	2161590	C-T	Hetero	INTERGENIC
SBS	Chr7	27032998	T-A	Hetero	NON_SYNONYMOUS_CODING	OsKitaake07g252700
SBS	Chr7	29041315	G-T	Hetero	INTERGENIC
SBS	Chr8	3427768	T-A	Homo	INTERGENIC
SBS	Chr8	6112875	G-A	Homo	UTR_3_PRIME
SBS	Chr8	25059665	G-T	Homo	INTRON
SBS	Chr9	8764891	A-G	Hetero	INTERGENIC
SBS	Chr9	10402616	C-T	Hetero	INTRON
SBS	Chr10	21619695	C-A	Hetero	INTERGENIC
SBS	Chr11	14901562	A-G	Hetero	INTERGENIC
SBS	Chr11	18429560	G-T	Hetero	INTERGENIC
SBS	Chr11	23911894	C-T	Homo	INTERGENIC
SBS	Chr11	26261052	C-T	Homo	INTERGENIC

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr6	15859	15860	1
Deletion	Chr11	2464612	2464613	1
Deletion	Chr8	3564129	3564130	1
Deletion	Chr11	4101816	4101824	8
Deletion	Chr5	7910001	7940000	29999
Deletion	Chr3	8497515	8497516	1
Deletion	Chr12	12301219	12301232	13
Deletion	Chr7	13701001	13726000	24999
Deletion	Chr10	18868801	18868802	1
Deletion	Chr10	20351563	20351566	3
Deletion	Chr7	25343952	25343953	1	OsKitaake07g229500
Deletion	Chr11	27496867	27496870	3
Deletion	Chr2	28172837	28172840	3
Deletion	Chr2	33419932	33419933	1
Deletion	Chr1	40963857	40963867	10	OsKitaake01g446900

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr10	176353	942475
Inversion	Chr10	176359	942488

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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