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Mutant Information

Mutant Name	FN1509-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN1509-S Alignment File
Seed Availability	Yes [Order Seeds]
Phenotype	TO:0000326 (Leaf Color) = Normal TO:0000137 (Days to heading) = Normal (Between 75% and 125%) TO:0000346 (Tiller number) = Normal (Between 75% and 125%) TO:0000430 (Germination Rate) = Low (Between 25% and 75%) For more information, please see this phenotype file

Variant Information

Single base substitutions: 42

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 15232632 A-T Hetero INTERGENIC
SBS Chr1 18090101 T-G Hetero INTERGENIC
SBS Chr1 18090103 T-C Hetero INTERGENIC
SBS Chr1 23644129 G-A Hetero INTERGENIC
SBS Chr2 10110403 A-C Hetero INTERGENIC
SBS Chr2 27909500 A-G Hetero INTERGENIC
SBS Chr2 28205139 G-C Hetero INTERGENIC
SBS Chr3 13241290 C-A Hetero INTERGENIC
SBS Chr3 22235998 A-G Homo INTERGENIC
SBS Chr3 29989694 G-T Hetero INTERGENIC
SBS Chr3 37309412 A-G Hetero INTERGENIC
SBS Chr4 11042070 A-G Homo INTERGENIC
SBS Chr4 16357718 C-T Hetero INTERGENIC
SBS Chr4 23109701 C-A Homo INTRON
SBS Chr4 24829355 C-T Hetero INTERGENIC
SBS Chr4 34463435 T-C Homo INTERGENIC
SBS Chr4 34865088 T-G Hetero INTERGENIC
SBS Chr5 12095128 C-T Hetero INTERGENIC
SBS Chr5 14828019 C-T Hetero INTERGENIC
SBS Chr5 21143364 C-T Hetero INTERGENIC
SBS Chr6 12520928 T-C Hetero INTRON
SBS Chr6 14932543 C-T Hetero INTERGENIC
SBS Chr6 15136596 C-T Hetero INTERGENIC
SBS Chr6 22963376 T-C Homo INTERGENIC
SBS Chr6 26077337 T-A Homo INTERGENIC
SBS Chr7 6698956 T-A Homo INTERGENIC
SBS Chr8 5181521 C-G Hetero UTR_3_PRIME
SBS Chr8 6490349 C-T Hetero INTERGENIC
SBS Chr8 7210850 C-T Hetero INTERGENIC
SBS Chr8 18410519 A-G Hetero INTERGENIC
SBS Chr8 19325386 C-T Hetero INTERGENIC
SBS Chr9 3074564 C-T Hetero INTERGENIC
SBS Chr9 5585459 C-A Hetero NON_SYNONYMOUS_CODING OsKitaake09g032133
SBS Chr9 11190426 G-A Hetero INTERGENIC
SBS Chr10 17678453 T-C Hetero INTERGENIC
SBS Chr11 14769863 C-T Hetero INTERGENIC
SBS Chr11 19185633 A-C Homo INTERGENIC
SBS Chr11 22103531 G-T Hetero INTERGENIC
SBS Chr11 23676181 A-G Hetero INTERGENIC
SBS Chr11 24042331 G-A Hetero INTERGENIC
SBS Chr12 2270523 A-G Homo INTERGENIC
SBS Chr12 24556583 G-A Hetero INTRON

Deletions: 28

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr11 172001 244000 71999 10
Deletion Chr7 668193 668194 1 OsKitaake07g008000
Deletion Chr7 1215749 1215750 1
Deletion Chr5 1520001 1533000 12999
Deletion Chr11 2858909 2858929 20
Deletion Chr6 4500810 4500813 3
Deletion Chr9 6286108 6286110 2
Deletion Chr8 6637001 6688000 50999 OsKitaake08g069000
Deletion Chr3 8363001 8509000 145999 17
Deletion Chr11 9342674 9342682 8
Deletion Chr3 13569294 13569308 14
Deletion Chr4 14192915 14192930 15
Deletion Chr6 15758741 15758897 156
Deletion Chr9 16026420 16026422 2
Deletion Chr5 20469354 20469358 4
Deletion Chr1 20969281 20969287 6
Deletion Chr11 23297126 23297129 3
Deletion Chr11 23339951 23339959 8
Deletion Chr2 24818001 24844000 25999 7
Deletion Chr2 25994401 25994416 15
Deletion Chr2 26001502 26001505 3 OsKitaake02g256800
Deletion Chr8 29298701 29299407 706
Deletion Chr7 29634447 29634448 1
Deletion Chr1 34428676 34428678 2
Deletion Chr4 36416442 36416445 3
Deletion Chr2 36660348 36660350 2
Deletion Chr3 37309310 37309314 4
Deletion Chr1 40285001 40334000 48999 8

Insertions: 6

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr2 36310210 36310214 3
Insertion Chr4 30329730 30329741 10
Insertion Chr5 29287059 29287063 3
Insertion Chr12 10016519 10016522 2
Insertion Chr1 38196203 38196210 6 OsKitaake01g407400
Insertion Chr12 10853863 10853868 4

Translocations: 4

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes

Translocation Chr8 7131860 Chr1 15648110
Translocation Chr8 7132403 Chr1 15648100
Translocation Chr8 11822014 Chr3 8371129
Translocation Chr12 12510697 Chr8 7132408 OsKitaake12g106801

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	15232632	A-T	Hetero	INTERGENIC
SBS	Chr1	18090101	T-G	Hetero	INTERGENIC
SBS	Chr1	18090103	T-C	Hetero	INTERGENIC
SBS	Chr1	23644129	G-A	Hetero	INTERGENIC
SBS	Chr2	10110403	A-C	Hetero	INTERGENIC
SBS	Chr2	27909500	A-G	Hetero	INTERGENIC
SBS	Chr2	28205139	G-C	Hetero	INTERGENIC
SBS	Chr3	13241290	C-A	Hetero	INTERGENIC
SBS	Chr3	22235998	A-G	Homo	INTERGENIC
SBS	Chr3	29989694	G-T	Hetero	INTERGENIC
SBS	Chr3	37309412	A-G	Hetero	INTERGENIC
SBS	Chr4	11042070	A-G	Homo	INTERGENIC
SBS	Chr4	16357718	C-T	Hetero	INTERGENIC
SBS	Chr4	23109701	C-A	Homo	INTRON
SBS	Chr4	24829355	C-T	Hetero	INTERGENIC
SBS	Chr4	34463435	T-C	Homo	INTERGENIC
SBS	Chr4	34865088	T-G	Hetero	INTERGENIC
SBS	Chr5	12095128	C-T	Hetero	INTERGENIC
SBS	Chr5	14828019	C-T	Hetero	INTERGENIC
SBS	Chr5	21143364	C-T	Hetero	INTERGENIC
SBS	Chr6	12520928	T-C	Hetero	INTRON
SBS	Chr6	14932543	C-T	Hetero	INTERGENIC
SBS	Chr6	15136596	C-T	Hetero	INTERGENIC
SBS	Chr6	22963376	T-C	Homo	INTERGENIC
SBS	Chr6	26077337	T-A	Homo	INTERGENIC
SBS	Chr7	6698956	T-A	Homo	INTERGENIC
SBS	Chr8	5181521	C-G	Hetero	UTR_3_PRIME
SBS	Chr8	6490349	C-T	Hetero	INTERGENIC
SBS	Chr8	7210850	C-T	Hetero	INTERGENIC
SBS	Chr8	18410519	A-G	Hetero	INTERGENIC
SBS	Chr8	19325386	C-T	Hetero	INTERGENIC
SBS	Chr9	3074564	C-T	Hetero	INTERGENIC
SBS	Chr9	5585459	C-A	Hetero	NON_SYNONYMOUS_CODING	OsKitaake09g032133
SBS	Chr9	11190426	G-A	Hetero	INTERGENIC
SBS	Chr10	17678453	T-C	Hetero	INTERGENIC
SBS	Chr11	14769863	C-T	Hetero	INTERGENIC
SBS	Chr11	19185633	A-C	Homo	INTERGENIC
SBS	Chr11	22103531	G-T	Hetero	INTERGENIC
SBS	Chr11	23676181	A-G	Hetero	INTERGENIC
SBS	Chr11	24042331	G-A	Hetero	INTERGENIC
SBS	Chr12	2270523	A-G	Homo	INTERGENIC
SBS	Chr12	24556583	G-A	Hetero	INTRON

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr11	172001	244000	71999	10
Deletion	Chr7	668193	668194	1	OsKitaake07g008000
Deletion	Chr7	1215749	1215750	1
Deletion	Chr5	1520001	1533000	12999
Deletion	Chr11	2858909	2858929	20
Deletion	Chr6	4500810	4500813	3
Deletion	Chr9	6286108	6286110	2
Deletion	Chr8	6637001	6688000	50999	OsKitaake08g069000
Deletion	Chr3	8363001	8509000	145999	17
Deletion	Chr11	9342674	9342682	8
Deletion	Chr3	13569294	13569308	14
Deletion	Chr4	14192915	14192930	15
Deletion	Chr6	15758741	15758897	156
Deletion	Chr9	16026420	16026422	2
Deletion	Chr5	20469354	20469358	4
Deletion	Chr1	20969281	20969287	6
Deletion	Chr11	23297126	23297129	3
Deletion	Chr11	23339951	23339959	8
Deletion	Chr2	24818001	24844000	25999	7
Deletion	Chr2	25994401	25994416	15
Deletion	Chr2	26001502	26001505	3	OsKitaake02g256800
Deletion	Chr8	29298701	29299407	706
Deletion	Chr7	29634447	29634448	1
Deletion	Chr1	34428676	34428678	2
Deletion	Chr4	36416442	36416445	3
Deletion	Chr2	36660348	36660350	2
Deletion	Chr3	37309310	37309314	4
Deletion	Chr1	40285001	40334000	48999	8

Variant Type	Chromosome	Position 1	Chromosome	Position 2	Number of Genes
Translocation	Chr8	7131860	Chr1	15648110
Translocation	Chr8	7132403	Chr1	15648100
Translocation	Chr8	11822014	Chr3	8371129
Translocation	Chr12	12510697	Chr8	7132408	OsKitaake12g106801

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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

Chromosome

Position 2

Number of Genes