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Mutant Information

Mutant Name	FN2477 [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN2477 Alignment File
Seed Availability	Yes [Order Seeds]
Phenotype	TO:0000430 (Germination Rate) = Normal (Between 75% and 125%) For more information, please see this phenotype file

Variant Information

Single base substitutions: 51

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 27346517 T-G Hetero INTERGENIC
SBS Chr1 36797159 C-T Hetero INTERGENIC
SBS Chr1 38338246 T-C Hetero INTERGENIC
SBS Chr2 1356240 T-A Homo UTR_3_PRIME
SBS Chr2 7360021 C-T Hetero INTERGENIC
SBS Chr2 10478132 A-C Hetero INTERGENIC
SBS Chr2 10484762 C-A Hetero INTERGENIC
SBS Chr2 18121874 G-T Hetero INTRON
SBS Chr2 18505447 G-A Hetero INTERGENIC
SBS Chr2 24284875 A-G Hetero INTERGENIC
SBS Chr2 26095662 G-A Hetero NON_SYNONYMOUS_CODING OsKitaake02g258100
SBS Chr3 5103768 G-A Homo INTERGENIC
SBS Chr3 6310728 T-A Homo INTERGENIC
SBS Chr3 7483169 G-T Homo INTRON
SBS Chr3 23701580 C-T Homo INTERGENIC
SBS Chr3 36036947 G-A Hetero INTERGENIC
SBS Chr4 10271979 T-C Homo INTERGENIC
SBS Chr4 21936879 T-C Hetero INTERGENIC
SBS Chr4 23527903 T-A Hetero NON_SYNONYMOUS_CODING OsKitaake04g147000
SBS Chr4 23527905 G-C Hetero NON_SYNONYMOUS_CODING OsKitaake04g147000
SBS Chr4 32936708 C-A Homo INTERGENIC
SBS Chr4 34443112 G-T Homo INTERGENIC
SBS Chr5 23486324 G-A Hetero INTERGENIC
SBS Chr6 4156805 G-A Hetero INTERGENIC
SBS Chr6 6799040 G-A Hetero INTERGENIC
SBS Chr6 14644181 C-T Hetero INTERGENIC
SBS Chr6 25323813 G-A Homo INTERGENIC
SBS Chr6 27405243 G-A Homo INTERGENIC
SBS Chr7 22965928 G-A Homo INTERGENIC
SBS Chr7 25207388 A-G Homo INTERGENIC
SBS Chr7 25938482 G-C Hetero NON_SYNONYMOUS_CODING OsKitaake07g237000
SBS Chr8 9495389 C-T Homo INTERGENIC
SBS Chr8 13214427 C-T Hetero INTERGENIC
SBS Chr8 21000874 G-A Hetero INTERGENIC
SBS Chr8 24197778 T-C Hetero NON_SYNONYMOUS_CODING OsKitaake08g187000
SBS Chr9 9420068 G-T Hetero SYNONYMOUS_CODING
SBS Chr10 3086840 G-A Homo INTERGENIC
SBS Chr10 7540146 C-G Hetero INTERGENIC
SBS Chr10 12537111 C-A Hetero UTR_5_PRIME
SBS Chr10 13145000 C-T Homo INTERGENIC
SBS Chr11 2853939 C-T Hetero INTERGENIC
SBS Chr11 12480095 G-A Hetero INTERGENIC
SBS Chr11 19863131 C-G Hetero INTERGENIC
SBS Chr11 23607466 T-G Hetero INTERGENIC
SBS Chr11 27578326 T-C Hetero INTERGENIC
SBS Chr11 28000748 C-T Homo INTERGENIC
SBS Chr12 1603015 C-T Hetero INTERGENIC
SBS Chr12 6272215 C-T Hetero INTERGENIC
SBS Chr12 9680715 C-A Hetero INTERGENIC
SBS Chr12 16707525 G-T Hetero INTERGENIC
SBS Chr12 19800245 G-A Hetero INTERGENIC

Deletions: 19

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr10 1943198 1943204 6 OsKitaake10g015300
Deletion Chr5 2097618 2097630 12
Deletion Chr2 4197694 4197698 4
Deletion Chr3 4800747 4800748 1
Deletion Chr2 5422620 5422629 9 OsKitaake02g074500
Deletion Chr6 7978428 7978431 3
Deletion Chr9 9619017 9619018 1
Deletion Chr4 10253446 10253454 8
Deletion Chr11 14121592 14121594 2
Deletion Chr12 17640545 17640551 6
Deletion Chr7 18146676 18146677 1
Deletion Chr4 20534895 20534903 8
Deletion Chr12 21061482 21061485 3 OsKitaake12g164700
Deletion Chr4 22069001 22087000 17999 OsKitaake04g129000
Deletion Chr11 23067205 23067210 5
Deletion Chr2 26640001 26695000 54999 7
Deletion Chr5 29082580 29082588 8
Deletion Chr3 35061600 35061607 7
Deletion Chr3 35901024 35901032 8

Insertions: 7

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr1 22920699 22920702 2
Insertion Chr1 31371435 31371438 2
Insertion Chr2 4084746 4084753 6
Insertion Chr2 8537531 8537534 2
Insertion Chr9 5733589 5733591 1
Insertion Chr11 21376013 21376016 2
Insertion Chr5 29939081 29939084 2

Inversions: 8

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Inversion Chr12 4343705 4773518
Inversion Chr12 4343711 4773521
Inversion Chr5 18216927 18655133 OsKitaake05g142000
Inversion Chr5 18216934 18655139 OsKitaake05g142000
Inversion Chr4 21939000 21974095 OsKitaake04g127200
Inversion Chr4 21939002 21974106 OsKitaake04g127200
Inversion Chr1 29070708 29797674 OsKitaake01g282300
Inversion Chr1 29078441 29797677

Translocations: 2

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes

Translocation Chr2 30719695 Chr1 29078432
Translocation Chr2 30719719 Chr1 29070737 OsKitaake01g282300

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	27346517	T-G	Hetero	INTERGENIC
SBS	Chr1	36797159	C-T	Hetero	INTERGENIC
SBS	Chr1	38338246	T-C	Hetero	INTERGENIC
SBS	Chr2	1356240	T-A	Homo	UTR_3_PRIME
SBS	Chr2	7360021	C-T	Hetero	INTERGENIC
SBS	Chr2	10478132	A-C	Hetero	INTERGENIC
SBS	Chr2	10484762	C-A	Hetero	INTERGENIC
SBS	Chr2	18121874	G-T	Hetero	INTRON
SBS	Chr2	18505447	G-A	Hetero	INTERGENIC
SBS	Chr2	24284875	A-G	Hetero	INTERGENIC
SBS	Chr2	26095662	G-A	Hetero	NON_SYNONYMOUS_CODING	OsKitaake02g258100
SBS	Chr3	5103768	G-A	Homo	INTERGENIC
SBS	Chr3	6310728	T-A	Homo	INTERGENIC
SBS	Chr3	7483169	G-T	Homo	INTRON
SBS	Chr3	23701580	C-T	Homo	INTERGENIC
SBS	Chr3	36036947	G-A	Hetero	INTERGENIC
SBS	Chr4	10271979	T-C	Homo	INTERGENIC
SBS	Chr4	21936879	T-C	Hetero	INTERGENIC
SBS	Chr4	23527903	T-A	Hetero	NON_SYNONYMOUS_CODING	OsKitaake04g147000
SBS	Chr4	23527905	G-C	Hetero	NON_SYNONYMOUS_CODING	OsKitaake04g147000
SBS	Chr4	32936708	C-A	Homo	INTERGENIC
SBS	Chr4	34443112	G-T	Homo	INTERGENIC
SBS	Chr5	23486324	G-A	Hetero	INTERGENIC
SBS	Chr6	4156805	G-A	Hetero	INTERGENIC
SBS	Chr6	6799040	G-A	Hetero	INTERGENIC
SBS	Chr6	14644181	C-T	Hetero	INTERGENIC
SBS	Chr6	25323813	G-A	Homo	INTERGENIC
SBS	Chr6	27405243	G-A	Homo	INTERGENIC
SBS	Chr7	22965928	G-A	Homo	INTERGENIC
SBS	Chr7	25207388	A-G	Homo	INTERGENIC
SBS	Chr7	25938482	G-C	Hetero	NON_SYNONYMOUS_CODING	OsKitaake07g237000
SBS	Chr8	9495389	C-T	Homo	INTERGENIC
SBS	Chr8	13214427	C-T	Hetero	INTERGENIC
SBS	Chr8	21000874	G-A	Hetero	INTERGENIC
SBS	Chr8	24197778	T-C	Hetero	NON_SYNONYMOUS_CODING	OsKitaake08g187000
SBS	Chr9	9420068	G-T	Hetero	SYNONYMOUS_CODING
SBS	Chr10	3086840	G-A	Homo	INTERGENIC
SBS	Chr10	7540146	C-G	Hetero	INTERGENIC
SBS	Chr10	12537111	C-A	Hetero	UTR_5_PRIME
SBS	Chr10	13145000	C-T	Homo	INTERGENIC
SBS	Chr11	2853939	C-T	Hetero	INTERGENIC
SBS	Chr11	12480095	G-A	Hetero	INTERGENIC
SBS	Chr11	19863131	C-G	Hetero	INTERGENIC
SBS	Chr11	23607466	T-G	Hetero	INTERGENIC
SBS	Chr11	27578326	T-C	Hetero	INTERGENIC
SBS	Chr11	28000748	C-T	Homo	INTERGENIC
SBS	Chr12	1603015	C-T	Hetero	INTERGENIC
SBS	Chr12	6272215	C-T	Hetero	INTERGENIC
SBS	Chr12	9680715	C-A	Hetero	INTERGENIC
SBS	Chr12	16707525	G-T	Hetero	INTERGENIC
SBS	Chr12	19800245	G-A	Hetero	INTERGENIC

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr10	1943198	1943204	6	OsKitaake10g015300
Deletion	Chr5	2097618	2097630	12
Deletion	Chr2	4197694	4197698	4
Deletion	Chr3	4800747	4800748	1
Deletion	Chr2	5422620	5422629	9	OsKitaake02g074500
Deletion	Chr6	7978428	7978431	3
Deletion	Chr9	9619017	9619018	1
Deletion	Chr4	10253446	10253454	8
Deletion	Chr11	14121592	14121594	2
Deletion	Chr12	17640545	17640551	6
Deletion	Chr7	18146676	18146677	1
Deletion	Chr4	20534895	20534903	8
Deletion	Chr12	21061482	21061485	3	OsKitaake12g164700
Deletion	Chr4	22069001	22087000	17999	OsKitaake04g129000
Deletion	Chr11	23067205	23067210	5
Deletion	Chr2	26640001	26695000	54999	7
Deletion	Chr5	29082580	29082588	8
Deletion	Chr3	35061600	35061607	7
Deletion	Chr3	35901024	35901032	8

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr12	4343705	4773518
Inversion	Chr12	4343711	4773521
Inversion	Chr5	18216927	18655133	OsKitaake05g142000
Inversion	Chr5	18216934	18655139	OsKitaake05g142000
Inversion	Chr4	21939000	21974095	OsKitaake04g127200
Inversion	Chr4	21939002	21974106	OsKitaake04g127200
Inversion	Chr1	29070708	29797674	OsKitaake01g282300
Inversion	Chr1	29078441	29797677

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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