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Mutant Information

Mutant Name	N1-169-5 [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download N1-169-5 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: 51

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 20476104 C-G Hetero INTERGENIC
SBS Chr1 23727003 G-A Hetero INTERGENIC
SBS Chr1 26085850 G-A Homo INTERGENIC
SBS Chr1 29427413 A-T Homo INTERGENIC
SBS Chr1 32694971 A-T Homo INTERGENIC
SBS Chr1 42597663 C-T Hetero INTERGENIC
SBS Chr2 17777239 G-A Hetero INTERGENIC
SBS Chr2 28657346 C-T Hetero INTERGENIC
SBS Chr2 30458717 A-T Homo SYNONYMOUS_CODING
SBS Chr2 34237655 A-G Homo INTERGENIC
SBS Chr3 12967649 A-T Hetero INTRON
SBS Chr3 27071850 G-A Hetero INTERGENIC
SBS Chr3 32010501 T-A Homo INTERGENIC
SBS Chr4 2830084 C-A Hetero INTERGENIC
SBS Chr4 5010429 G-T Homo INTERGENIC
SBS Chr4 7539500 A-G Homo INTERGENIC
SBS Chr4 31659425 G-A Homo UTR_3_PRIME
SBS Chr4 31659426 C-A Homo UTR_3_PRIME
SBS Chr4 33690266 G-A Hetero INTERGENIC
SBS Chr5 3136458 A-T Hetero INTERGENIC
SBS Chr5 5884249 C-G Hetero INTERGENIC
SBS Chr5 11454918 G-A Hetero INTERGENIC
SBS Chr5 13589729 G-A Hetero INTERGENIC
SBS Chr5 27736468 C-T Homo INTRON
SBS Chr5 27736469 G-A Homo INTRON
SBS Chr6 10840802 C-A Hetero INTERGENIC
SBS Chr6 12955525 T-A Hetero INTERGENIC
SBS Chr6 20327187 G-A Homo INTRON
SBS Chr7 6624447 T-C Hetero INTERGENIC
SBS Chr7 14317356 C-T Hetero INTRON
SBS Chr8 509201 C-T Hetero INTERGENIC
SBS Chr8 25977114 A-T Homo INTERGENIC
SBS Chr9 5484440 T-A Homo INTERGENIC
SBS Chr10 1019831 T-A Hetero INTERGENIC
SBS Chr10 5336431 C-T Hetero INTERGENIC
SBS Chr10 6127391 G-A Hetero INTERGENIC
SBS Chr10 19567459 G-A Homo SYNONYMOUS_CODING
SBS Chr10 19580590 C-G Homo UTR_3_PRIME
SBS Chr10 19972193 A-C Hetero INTERGENIC
SBS Chr11 4153128 G-C Hetero INTERGENIC
SBS Chr11 5396582 T-A Homo INTERGENIC
SBS Chr11 16125326 C-A Hetero INTERGENIC
SBS Chr11 16230898 G-C Homo INTERGENIC
SBS Chr11 18997349 G-C Hetero INTERGENIC
SBS Chr11 26482651 G-A Homo INTERGENIC
SBS Chr11 27221269 G-A Hetero INTERGENIC
SBS Chr12 11827347 A-T Hetero INTERGENIC
SBS Chr12 12268576 T-A Hetero INTERGENIC
SBS Chr12 14743116 A-T Hetero INTERGENIC
SBS Chr12 17156339 G-A Hetero INTERGENIC
SBS Chr12 20185679 G-C Homo INTERGENIC

Deletions: 15

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr6 4130063 4130064 1
Deletion Chr6 8324418 8324420 2
Deletion Chr12 19639777 19639781 4 OsKitaake12g147600
Deletion Chr6 20564524 20564534 10
Deletion Chr12 21054678 21054680 2
Deletion Chr9 21919001 22216000 296999 63
Deletion Chr6 21954658 21954659 1
Deletion Chr5 23239191 23239201 10
Deletion Chr2 23429427 23429436 9 OsKitaake02g229500
Deletion Chr5 25759113 25759115 2
Deletion Chr8 25945732 25945747 15
Deletion Chr2 28605688 28605689 1
Deletion Chr2 33235848 33235856 8
Deletion Chr3 35517001 35526000 8999
Deletion Chr1 40156569 40156575 6

Insertions: 3

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr4 1061702 1061705 2
Insertion Chr7 17400373 17400376 2
Insertion Chr4 13238148 13238150 1

Inversions: 8

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Inversion Chr8 4094109 4176193
Inversion Chr8 4094114 4176195
Inversion Chr2 7350343 7583844 2
Inversion Chr2 7350687 7679619 OsKitaake02g100500
Inversion Chr2 7583954 7679596 2
Inversion Chr2 7584070 7666802 OsKitaake02g099900
Inversion Chr1 33759873 34048605 OsKitaake01g350400
Inversion Chr1 33831528 34048604 2

Translocations: 5

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes

Translocation Chr11 6915778 Chr2 7350679 OsKitaake02g098100
Translocation Chr12 19052738 Chr11 16382972 OsKitaake11g130300
Translocation Chr9 21920581 Chr4 26505278 OsKitaake04g190400
Translocation Chr9 22209706 Chr4 26505284 OsKitaake04g190400
Translocation Chr4 25617951 Chr2 7666795

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	20476104	C-G	Hetero	INTERGENIC
SBS	Chr1	23727003	G-A	Hetero	INTERGENIC
SBS	Chr1	26085850	G-A	Homo	INTERGENIC
SBS	Chr1	29427413	A-T	Homo	INTERGENIC
SBS	Chr1	32694971	A-T	Homo	INTERGENIC
SBS	Chr1	42597663	C-T	Hetero	INTERGENIC
SBS	Chr2	17777239	G-A	Hetero	INTERGENIC
SBS	Chr2	28657346	C-T	Hetero	INTERGENIC
SBS	Chr2	30458717	A-T	Homo	SYNONYMOUS_CODING
SBS	Chr2	34237655	A-G	Homo	INTERGENIC
SBS	Chr3	12967649	A-T	Hetero	INTRON
SBS	Chr3	27071850	G-A	Hetero	INTERGENIC
SBS	Chr3	32010501	T-A	Homo	INTERGENIC
SBS	Chr4	2830084	C-A	Hetero	INTERGENIC
SBS	Chr4	5010429	G-T	Homo	INTERGENIC
SBS	Chr4	7539500	A-G	Homo	INTERGENIC
SBS	Chr4	31659425	G-A	Homo	UTR_3_PRIME
SBS	Chr4	31659426	C-A	Homo	UTR_3_PRIME
SBS	Chr4	33690266	G-A	Hetero	INTERGENIC
SBS	Chr5	3136458	A-T	Hetero	INTERGENIC
SBS	Chr5	5884249	C-G	Hetero	INTERGENIC
SBS	Chr5	11454918	G-A	Hetero	INTERGENIC
SBS	Chr5	13589729	G-A	Hetero	INTERGENIC
SBS	Chr5	27736468	C-T	Homo	INTRON
SBS	Chr5	27736469	G-A	Homo	INTRON
SBS	Chr6	10840802	C-A	Hetero	INTERGENIC
SBS	Chr6	12955525	T-A	Hetero	INTERGENIC
SBS	Chr6	20327187	G-A	Homo	INTRON
SBS	Chr7	6624447	T-C	Hetero	INTERGENIC
SBS	Chr7	14317356	C-T	Hetero	INTRON
SBS	Chr8	509201	C-T	Hetero	INTERGENIC
SBS	Chr8	25977114	A-T	Homo	INTERGENIC
SBS	Chr9	5484440	T-A	Homo	INTERGENIC
SBS	Chr10	1019831	T-A	Hetero	INTERGENIC
SBS	Chr10	5336431	C-T	Hetero	INTERGENIC
SBS	Chr10	6127391	G-A	Hetero	INTERGENIC
SBS	Chr10	19567459	G-A	Homo	SYNONYMOUS_CODING
SBS	Chr10	19580590	C-G	Homo	UTR_3_PRIME
SBS	Chr10	19972193	A-C	Hetero	INTERGENIC
SBS	Chr11	4153128	G-C	Hetero	INTERGENIC
SBS	Chr11	5396582	T-A	Homo	INTERGENIC
SBS	Chr11	16125326	C-A	Hetero	INTERGENIC
SBS	Chr11	16230898	G-C	Homo	INTERGENIC
SBS	Chr11	18997349	G-C	Hetero	INTERGENIC
SBS	Chr11	26482651	G-A	Homo	INTERGENIC
SBS	Chr11	27221269	G-A	Hetero	INTERGENIC
SBS	Chr12	11827347	A-T	Hetero	INTERGENIC
SBS	Chr12	12268576	T-A	Hetero	INTERGENIC
SBS	Chr12	14743116	A-T	Hetero	INTERGENIC
SBS	Chr12	17156339	G-A	Hetero	INTERGENIC
SBS	Chr12	20185679	G-C	Homo	INTERGENIC

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr6	4130063	4130064	1
Deletion	Chr6	8324418	8324420	2
Deletion	Chr12	19639777	19639781	4	OsKitaake12g147600
Deletion	Chr6	20564524	20564534	10
Deletion	Chr12	21054678	21054680	2
Deletion	Chr9	21919001	22216000	296999	63
Deletion	Chr6	21954658	21954659	1
Deletion	Chr5	23239191	23239201	10
Deletion	Chr2	23429427	23429436	9	OsKitaake02g229500
Deletion	Chr5	25759113	25759115	2
Deletion	Chr8	25945732	25945747	15
Deletion	Chr2	28605688	28605689	1
Deletion	Chr2	33235848	33235856	8
Deletion	Chr3	35517001	35526000	8999
Deletion	Chr1	40156569	40156575	6

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr8	4094109	4176193
Inversion	Chr8	4094114	4176195
Inversion	Chr2	7350343	7583844	2
Inversion	Chr2	7350687	7679619	OsKitaake02g100500
Inversion	Chr2	7583954	7679596	2
Inversion	Chr2	7584070	7666802	OsKitaake02g099900
Inversion	Chr1	33759873	34048605	OsKitaake01g350400
Inversion	Chr1	33831528	34048604	2

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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