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Mutant Information

Mutant Name	FN2976-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN2976-S Alignment File
Seed Availability	Yes [Order Seeds]
Phenotype	TO:0000430 (Germination Rate) = Low (Between 25% and 75%) For more information, please see this phenotype file

Variant Information

Single base substitutions: 63

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 18915600 C-T Hetero INTERGENIC
SBS Chr1 25777601 G-A Hetero UTR_5_PRIME
SBS Chr1 26261276 T-A Homo INTERGENIC
SBS Chr1 30296064 G-T Hetero INTRON
SBS Chr1 31350969 A-T Hetero INTERGENIC
SBS Chr1 40201805 G-A Hetero INTRON
SBS Chr1 41275575 T-A Hetero INTERGENIC
SBS Chr2 5525454 C-T Hetero INTERGENIC
SBS Chr2 11434143 T-C Hetero INTRON
SBS Chr2 11708828 C-T Hetero INTERGENIC
SBS Chr2 14189332 C-T Hetero STOP_GAINED OsKitaake02g152500
SBS Chr2 15509755 C-T Hetero INTERGENIC
SBS Chr2 18598900 G-A Hetero INTERGENIC
SBS Chr2 24902667 G-C Hetero INTERGENIC
SBS Chr2 25816329 C-T Hetero SYNONYMOUS_CODING
SBS Chr2 26280365 A-T Hetero INTERGENIC
SBS Chr2 27637241 C-T Hetero INTERGENIC
SBS Chr2 30269519 A-G Hetero INTERGENIC
SBS Chr2 33158128 G-A Hetero INTERGENIC
SBS Chr2 36297367 C-A Hetero INTERGENIC
SBS Chr3 14025116 G-A Hetero INTERGENIC
SBS Chr3 14993755 T-C Hetero INTERGENIC
SBS Chr3 34815078 T-C Homo INTERGENIC
SBS Chr4 1671598 G-A Hetero INTERGENIC
SBS Chr4 2814982 C-T Hetero INTERGENIC
SBS Chr4 26894515 G-T Hetero INTRON
SBS Chr5 279120 T-A Hetero STOP_GAINED OsKitaake05g003800
SBS Chr5 3636343 C-T Hetero INTERGENIC
SBS Chr5 9756713 A-G Hetero INTERGENIC
SBS Chr5 17005189 C-G Homo INTERGENIC
SBS Chr6 24463226 C-A Homo INTERGENIC
SBS Chr6 25022628 G-A Hetero INTERGENIC
SBS Chr6 26734141 T-C Hetero UTR_5_PRIME
SBS Chr6 29371515 G-A Hetero NON_SYNONYMOUS_CODING OsKitaake06g272100
SBS Chr7 373533 G-A Hetero INTERGENIC
SBS Chr7 9101075 G-C Hetero INTERGENIC
SBS Chr7 16465413 A-C Hetero INTERGENIC
SBS Chr8 12339536 G-A Hetero INTERGENIC
SBS Chr8 15730242 A-G Hetero INTERGENIC
SBS Chr8 16851864 C-T Homo INTERGENIC
SBS Chr8 19344225 G-A Hetero INTERGENIC
SBS Chr8 26902607 T-C Hetero INTERGENIC
SBS Chr8 27936054 C-T Hetero INTERGENIC
SBS Chr8 28919780 G-A Hetero INTERGENIC
SBS Chr9 8886194 G-A Hetero INTERGENIC
SBS Chr9 10643656 T-G Hetero INTERGENIC
SBS Chr9 16637609 A-T Hetero INTRON
SBS Chr10 3807753 C-T Hetero INTERGENIC
SBS Chr10 4305422 C-T Hetero INTERGENIC
SBS Chr10 8908783 G-A Hetero INTERGENIC
SBS Chr10 9436941 T-G Hetero INTERGENIC
SBS Chr10 22485399 G-A Hetero INTERGENIC
SBS Chr11 5790642 G-C Hetero INTERGENIC
SBS Chr11 8618207 A-G Hetero INTERGENIC
SBS Chr11 11851772 C-T Hetero INTERGENIC
SBS Chr11 15100751 C-T Hetero INTERGENIC
SBS Chr11 20732485 G-C Homo INTERGENIC
SBS Chr11 28474280 T-C Hetero INTERGENIC
SBS Chr12 6670352 C-G Hetero INTERGENIC
SBS Chr12 7041307 G-A Homo INTERGENIC
SBS Chr12 22340612 C-T Hetero INTERGENIC
SBS Chr12 23122225 C-T Hetero NON_SYNONYMOUS_CODING OsKitaake12g184500
SBS Chr12 24856973 C-T Hetero INTRON

Deletions: 21

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr5 4121721 4121723 2
Deletion Chr3 8259521 8259549 28
Deletion Chr4 8737457 8737459 2
Deletion Chr10 9846724 9846726 2
Deletion Chr3 11601914 11601915 1
Deletion Chr10 13218574 13218579 5
Deletion Chr8 13598612 13598614 2
Deletion Chr7 16487716 16487719 3 OsKitaake07g135600
Deletion Chr10 16943608 16943621 13
Deletion Chr12 18857659 18857663 4
Deletion Chr2 19905001 20901000 995999 92
Deletion Chr4 20675308 20675309 1
Deletion Chr2 22859370 22859372 2
Deletion Chr7 23982323 23982324 1
Deletion Chr1 25779001 25855000 75999 14
Deletion Chr1 25861001 26227000 365999 43
Deletion Chr12 26107316 26107324 8
Deletion Chr1 26232001 26350000 117999 9
Deletion Chr2 33280578 33280580 2
Deletion Chr1 34634001 34735000 100999 24
Deletion Chr1 35172038 35172050 12

Insertions: 5

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr1 20847101 20847104 2
Insertion Chr2 10549705 10549707 1
Insertion Chr3 5367069 5367074 4
Insertion Chr10 20245590 20245595 4
Insertion Chr12 17628256 17628260 3

Inversions: 4

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Inversion Chr9 16622542 16635624 OsKitaake09g121900
Inversion Chr9 16622567 16636979 OsKitaake09g121900
Inversion Chr1 25471515 25783788 2
Inversion Chr1 34636393 34781276 OsKitaake01g363400

Translocations: 2

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes

Translocation Chr9 16635637 Chr1 34781305 OsKitaake09g121900
Translocation Chr9 16636966 Chr1 34732719 OsKitaake09g121900

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	18915600	C-T	Hetero	INTERGENIC
SBS	Chr1	25777601	G-A	Hetero	UTR_5_PRIME
SBS	Chr1	26261276	T-A	Homo	INTERGENIC
SBS	Chr1	30296064	G-T	Hetero	INTRON
SBS	Chr1	31350969	A-T	Hetero	INTERGENIC
SBS	Chr1	40201805	G-A	Hetero	INTRON
SBS	Chr1	41275575	T-A	Hetero	INTERGENIC
SBS	Chr2	5525454	C-T	Hetero	INTERGENIC
SBS	Chr2	11434143	T-C	Hetero	INTRON
SBS	Chr2	11708828	C-T	Hetero	INTERGENIC
SBS	Chr2	14189332	C-T	Hetero	STOP_GAINED	OsKitaake02g152500
SBS	Chr2	15509755	C-T	Hetero	INTERGENIC
SBS	Chr2	18598900	G-A	Hetero	INTERGENIC
SBS	Chr2	24902667	G-C	Hetero	INTERGENIC
SBS	Chr2	25816329	C-T	Hetero	SYNONYMOUS_CODING
SBS	Chr2	26280365	A-T	Hetero	INTERGENIC
SBS	Chr2	27637241	C-T	Hetero	INTERGENIC
SBS	Chr2	30269519	A-G	Hetero	INTERGENIC
SBS	Chr2	33158128	G-A	Hetero	INTERGENIC
SBS	Chr2	36297367	C-A	Hetero	INTERGENIC
SBS	Chr3	14025116	G-A	Hetero	INTERGENIC
SBS	Chr3	14993755	T-C	Hetero	INTERGENIC
SBS	Chr3	34815078	T-C	Homo	INTERGENIC
SBS	Chr4	1671598	G-A	Hetero	INTERGENIC
SBS	Chr4	2814982	C-T	Hetero	INTERGENIC
SBS	Chr4	26894515	G-T	Hetero	INTRON
SBS	Chr5	279120	T-A	Hetero	STOP_GAINED	OsKitaake05g003800
SBS	Chr5	3636343	C-T	Hetero	INTERGENIC
SBS	Chr5	9756713	A-G	Hetero	INTERGENIC
SBS	Chr5	17005189	C-G	Homo	INTERGENIC
SBS	Chr6	24463226	C-A	Homo	INTERGENIC
SBS	Chr6	25022628	G-A	Hetero	INTERGENIC
SBS	Chr6	26734141	T-C	Hetero	UTR_5_PRIME
SBS	Chr6	29371515	G-A	Hetero	NON_SYNONYMOUS_CODING	OsKitaake06g272100
SBS	Chr7	373533	G-A	Hetero	INTERGENIC
SBS	Chr7	9101075	G-C	Hetero	INTERGENIC
SBS	Chr7	16465413	A-C	Hetero	INTERGENIC
SBS	Chr8	12339536	G-A	Hetero	INTERGENIC
SBS	Chr8	15730242	A-G	Hetero	INTERGENIC
SBS	Chr8	16851864	C-T	Homo	INTERGENIC
SBS	Chr8	19344225	G-A	Hetero	INTERGENIC
SBS	Chr8	26902607	T-C	Hetero	INTERGENIC
SBS	Chr8	27936054	C-T	Hetero	INTERGENIC
SBS	Chr8	28919780	G-A	Hetero	INTERGENIC
SBS	Chr9	8886194	G-A	Hetero	INTERGENIC
SBS	Chr9	10643656	T-G	Hetero	INTERGENIC
SBS	Chr9	16637609	A-T	Hetero	INTRON
SBS	Chr10	3807753	C-T	Hetero	INTERGENIC
SBS	Chr10	4305422	C-T	Hetero	INTERGENIC
SBS	Chr10	8908783	G-A	Hetero	INTERGENIC
SBS	Chr10	9436941	T-G	Hetero	INTERGENIC
SBS	Chr10	22485399	G-A	Hetero	INTERGENIC
SBS	Chr11	5790642	G-C	Hetero	INTERGENIC
SBS	Chr11	8618207	A-G	Hetero	INTERGENIC
SBS	Chr11	11851772	C-T	Hetero	INTERGENIC
SBS	Chr11	15100751	C-T	Hetero	INTERGENIC
SBS	Chr11	20732485	G-C	Homo	INTERGENIC
SBS	Chr11	28474280	T-C	Hetero	INTERGENIC
SBS	Chr12	6670352	C-G	Hetero	INTERGENIC
SBS	Chr12	7041307	G-A	Homo	INTERGENIC
SBS	Chr12	22340612	C-T	Hetero	INTERGENIC
SBS	Chr12	23122225	C-T	Hetero	NON_SYNONYMOUS_CODING	OsKitaake12g184500
SBS	Chr12	24856973	C-T	Hetero	INTRON

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr5	4121721	4121723	2
Deletion	Chr3	8259521	8259549	28
Deletion	Chr4	8737457	8737459	2
Deletion	Chr10	9846724	9846726	2
Deletion	Chr3	11601914	11601915	1
Deletion	Chr10	13218574	13218579	5
Deletion	Chr8	13598612	13598614	2
Deletion	Chr7	16487716	16487719	3	OsKitaake07g135600
Deletion	Chr10	16943608	16943621	13
Deletion	Chr12	18857659	18857663	4
Deletion	Chr2	19905001	20901000	995999	92
Deletion	Chr4	20675308	20675309	1
Deletion	Chr2	22859370	22859372	2
Deletion	Chr7	23982323	23982324	1
Deletion	Chr1	25779001	25855000	75999	14
Deletion	Chr1	25861001	26227000	365999	43
Deletion	Chr12	26107316	26107324	8
Deletion	Chr1	26232001	26350000	117999	9
Deletion	Chr2	33280578	33280580	2
Deletion	Chr1	34634001	34735000	100999	24
Deletion	Chr1	35172038	35172050	12

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr9	16622542	16635624	OsKitaake09g121900
Inversion	Chr9	16622567	16636979	OsKitaake09g121900
Inversion	Chr1	25471515	25783788	2
Inversion	Chr1	34636393	34781276	OsKitaake01g363400

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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