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Mutant Information

Mutant Name	FN1346-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN1346-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) = Normal (Between 75% and 125%) For more information, please see this phenotype file

Variant Information

Single base substitutions: 48

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 2127547 C-T Hetero INTERGENIC
SBS Chr1 13415108 C-A Hetero INTERGENIC
SBS Chr1 17539961 A-G Hetero INTERGENIC
SBS Chr1 27068237 G-A Hetero INTERGENIC
SBS Chr1 31840591 A-T Hetero INTERGENIC
SBS Chr1 41055137 G-A Hetero INTRON
SBS Chr2 13977856 G-A Hetero INTERGENIC
SBS Chr2 28999173 G-A Hetero INTERGENIC
SBS Chr2 31841239 G-A Hetero INTERGENIC
SBS Chr3 15179650 C-T Homo INTERGENIC
SBS Chr3 16421072 G-A Hetero INTERGENIC
SBS Chr3 35695586 G-A Homo INTERGENIC
SBS Chr4 2057267 A-G Hetero INTERGENIC
SBS Chr4 11796774 G-T Hetero INTERGENIC
SBS Chr4 14806765 C-T Hetero INTERGENIC
SBS Chr4 19192535 T-C Hetero INTERGENIC
SBS Chr4 34686414 G-A Homo INTERGENIC
SBS Chr5 2017154 G-A Homo INTERGENIC
SBS Chr5 12352351 G-A Hetero INTERGENIC
SBS Chr5 23846914 A-G Homo INTERGENIC
SBS Chr6 5767574 C-T Hetero INTERGENIC
SBS Chr6 5991554 T-C Hetero INTERGENIC
SBS Chr6 13752705 C-T Hetero NON_SYNONYMOUS_CODING OsKitaake06g143700
SBS Chr6 26372330 A-G Homo SYNONYMOUS_CODING
SBS Chr6 26372331 G-A Homo NON_SYNONYMOUS_CODING OsKitaake06g236600
SBS Chr6 26372332 G-T Homo NON_SYNONYMOUS_CODING OsKitaake06g236600
SBS Chr7 5396009 C-G Homo INTRON
SBS Chr7 10808777 G-C Homo INTERGENIC
SBS Chr7 10818144 T-A Homo INTERGENIC
SBS Chr7 10818146 T-A Homo INTERGENIC
SBS Chr7 10818147 G-A Homo INTERGENIC
SBS Chr7 12448554 T-A Homo INTERGENIC
SBS Chr8 16416044 C-A Hetero INTERGENIC
SBS Chr8 24130662 G-A Homo INTERGENIC
SBS Chr9 12742938 T-C Homo INTERGENIC
SBS Chr9 13259802 G-A Homo INTRON
SBS Chr9 18122225 A-G Hetero INTERGENIC
SBS Chr10 3150269 T-A Hetero INTERGENIC
SBS Chr10 3150270 C-A Hetero INTERGENIC
SBS Chr10 11839833 G-A Hetero INTERGENIC
SBS Chr10 12225983 C-T Hetero INTERGENIC
SBS Chr10 18329021 A-T Homo INTERGENIC
SBS Chr10 18771535 G-A Hetero INTERGENIC
SBS Chr11 4517502 G-A Hetero INTERGENIC
SBS Chr11 9067236 T-A Hetero UTR_3_PRIME
SBS Chr11 10688453 C-A Hetero INTRON
SBS Chr11 15524881 T-C Hetero INTERGENIC
SBS Chr12 26390667 A-G Homo INTERGENIC

Deletions: 27

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr6 622174 622180 6
Deletion Chr7 1830170 1830173 3
Deletion Chr5 2861198 2861200 2
Deletion Chr10 4436438 4436439 1
Deletion Chr3 4577061 4577062 1
Deletion Chr11 5911507 5911508 1
Deletion Chr12 6805694 6805696 2
Deletion Chr3 7418234 7418236 2
Deletion Chr4 7706954 7706955 1
Deletion Chr4 10510001 10517000 6999
Deletion Chr1 10570941 10570943 2
Deletion Chr7 12234489 12234500 11
Deletion Chr10 13826943 13826952 9
Deletion Chr2 14061537 14061542 5
Deletion Chr12 15506820 15506821 1
Deletion Chr4 17006248 17006259 11
Deletion Chr10 17364001 17368000 3999
Deletion Chr6 18099415 18099541 126
Deletion Chr3 19789091 19789094 3
Deletion Chr9 20390774 20390778 4
Deletion Chr3 22195581 22195593 12
Deletion Chr3 25051371 25051377 6
Deletion Chr6 26401364 26401365 1
Deletion Chr4 32517473 32517478 5 OsKitaake04g260400
Deletion Chr4 34748045 34748192 147
Deletion Chr1 34840513 34840519 6
Deletion Chr1 42573134 42573143 9

Insertions: 11

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr1 13087880 13087883 2
Insertion Chr1 29549433 29549436 2
Insertion Chr3 16016445 16016447 1
Insertion Chr4 6752164 6752166 1
Insertion Chr6 3314139 3314142 2
Insertion Chr6 3986200 3986202 1
Insertion Chr8 18106716 18106723 6
Insertion Chr9 15395378 15395381 2
Insertion Chr10 20239395 20239399 3
Insertion Chr11 19013479 19013483 3
Insertion Chr8 13240636 13240647 10

Inversions: 6

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Inversion Chr11 9536661 9572743 OsKitaake11g099701
Inversion Chr11 9536670 9572753 OsKitaake11g099701
Inversion Chr10 17330354 17361403
Inversion Chr10 17330360 17368350
Inversion Chr3 19066796 19198601
Inversion Chr3 19066801 19821240

Translocations: 9

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes

Translocation Chr5 517939 Chr3 19198138
Translocation Chr7 7632114 Chr3 18587085
Translocation Chr12 11832370 Chr5 4771494
Translocation Chr10 17330361 Chr3 18587085
Translocation Chr10 17361415 Chr1 41175424 OsKitaake01g449500
Translocation Chr10 17363351 Chr1 41175415 OsKitaake01g449500
Translocation Chr10 17368350 Chr3 18587146
Translocation Chr8 25626582 Chr3 18587176 OsKitaake08g202700
Translocation Chr8 25626866 Chr3 18587083 OsKitaake08g202700

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	2127547	C-T	Hetero	INTERGENIC
SBS	Chr1	13415108	C-A	Hetero	INTERGENIC
SBS	Chr1	17539961	A-G	Hetero	INTERGENIC
SBS	Chr1	27068237	G-A	Hetero	INTERGENIC
SBS	Chr1	31840591	A-T	Hetero	INTERGENIC
SBS	Chr1	41055137	G-A	Hetero	INTRON
SBS	Chr2	13977856	G-A	Hetero	INTERGENIC
SBS	Chr2	28999173	G-A	Hetero	INTERGENIC
SBS	Chr2	31841239	G-A	Hetero	INTERGENIC
SBS	Chr3	15179650	C-T	Homo	INTERGENIC
SBS	Chr3	16421072	G-A	Hetero	INTERGENIC
SBS	Chr3	35695586	G-A	Homo	INTERGENIC
SBS	Chr4	2057267	A-G	Hetero	INTERGENIC
SBS	Chr4	11796774	G-T	Hetero	INTERGENIC
SBS	Chr4	14806765	C-T	Hetero	INTERGENIC
SBS	Chr4	19192535	T-C	Hetero	INTERGENIC
SBS	Chr4	34686414	G-A	Homo	INTERGENIC
SBS	Chr5	2017154	G-A	Homo	INTERGENIC
SBS	Chr5	12352351	G-A	Hetero	INTERGENIC
SBS	Chr5	23846914	A-G	Homo	INTERGENIC
SBS	Chr6	5767574	C-T	Hetero	INTERGENIC
SBS	Chr6	5991554	T-C	Hetero	INTERGENIC
SBS	Chr6	13752705	C-T	Hetero	NON_SYNONYMOUS_CODING	OsKitaake06g143700
SBS	Chr6	26372330	A-G	Homo	SYNONYMOUS_CODING
SBS	Chr6	26372331	G-A	Homo	NON_SYNONYMOUS_CODING	OsKitaake06g236600
SBS	Chr6	26372332	G-T	Homo	NON_SYNONYMOUS_CODING	OsKitaake06g236600
SBS	Chr7	5396009	C-G	Homo	INTRON
SBS	Chr7	10808777	G-C	Homo	INTERGENIC
SBS	Chr7	10818144	T-A	Homo	INTERGENIC
SBS	Chr7	10818146	T-A	Homo	INTERGENIC
SBS	Chr7	10818147	G-A	Homo	INTERGENIC
SBS	Chr7	12448554	T-A	Homo	INTERGENIC
SBS	Chr8	16416044	C-A	Hetero	INTERGENIC
SBS	Chr8	24130662	G-A	Homo	INTERGENIC
SBS	Chr9	12742938	T-C	Homo	INTERGENIC
SBS	Chr9	13259802	G-A	Homo	INTRON
SBS	Chr9	18122225	A-G	Hetero	INTERGENIC
SBS	Chr10	3150269	T-A	Hetero	INTERGENIC
SBS	Chr10	3150270	C-A	Hetero	INTERGENIC
SBS	Chr10	11839833	G-A	Hetero	INTERGENIC
SBS	Chr10	12225983	C-T	Hetero	INTERGENIC
SBS	Chr10	18329021	A-T	Homo	INTERGENIC
SBS	Chr10	18771535	G-A	Hetero	INTERGENIC
SBS	Chr11	4517502	G-A	Hetero	INTERGENIC
SBS	Chr11	9067236	T-A	Hetero	UTR_3_PRIME
SBS	Chr11	10688453	C-A	Hetero	INTRON
SBS	Chr11	15524881	T-C	Hetero	INTERGENIC
SBS	Chr12	26390667	A-G	Homo	INTERGENIC

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr6	622174	622180	6
Deletion	Chr7	1830170	1830173	3
Deletion	Chr5	2861198	2861200	2
Deletion	Chr10	4436438	4436439	1
Deletion	Chr3	4577061	4577062	1
Deletion	Chr11	5911507	5911508	1
Deletion	Chr12	6805694	6805696	2
Deletion	Chr3	7418234	7418236	2
Deletion	Chr4	7706954	7706955	1
Deletion	Chr4	10510001	10517000	6999
Deletion	Chr1	10570941	10570943	2
Deletion	Chr7	12234489	12234500	11
Deletion	Chr10	13826943	13826952	9
Deletion	Chr2	14061537	14061542	5
Deletion	Chr12	15506820	15506821	1
Deletion	Chr4	17006248	17006259	11
Deletion	Chr10	17364001	17368000	3999
Deletion	Chr6	18099415	18099541	126
Deletion	Chr3	19789091	19789094	3
Deletion	Chr9	20390774	20390778	4
Deletion	Chr3	22195581	22195593	12
Deletion	Chr3	25051371	25051377	6
Deletion	Chr6	26401364	26401365	1
Deletion	Chr4	32517473	32517478	5	OsKitaake04g260400
Deletion	Chr4	34748045	34748192	147
Deletion	Chr1	34840513	34840519	6
Deletion	Chr1	42573134	42573143	9

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr11	9536661	9572743	OsKitaake11g099701
Inversion	Chr11	9536670	9572753	OsKitaake11g099701
Inversion	Chr10	17330354	17361403
Inversion	Chr10	17330360	17368350
Inversion	Chr3	19066796	19198601
Inversion	Chr3	19066801	19821240

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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