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Mutant Information

Mutant Name	FN1339-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN1339-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: 51

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 17925345 C-T Homo NON_SYNONYMOUS_CODING OsKitaake01g181800
SBS Chr1 27369506 C-T Hetero INTERGENIC
SBS Chr2 11476635 C-T Homo INTERGENIC
SBS Chr2 26683011 T-G Hetero INTERGENIC
SBS Chr3 1928613 C-A Hetero NON_SYNONYMOUS_CODING OsKitaake03g027600
SBS Chr3 6525226 C-T Hetero INTERGENIC
SBS Chr3 6792697 C-G Hetero INTERGENIC
SBS Chr3 28827010 C-T Hetero INTERGENIC
SBS Chr3 36243489 T-C Hetero INTERGENIC
SBS Chr4 8752127 T-C Hetero UTR_3_PRIME
SBS Chr4 9916519 C-G Hetero INTERGENIC
SBS Chr4 10218421 C-T Hetero INTERGENIC
SBS Chr4 11131560 G-T Hetero INTERGENIC
SBS Chr4 13965682 A-C Hetero INTRON
SBS Chr4 17744824 G-A Hetero NON_SYNONYMOUS_CODING OsKitaake04g088900
SBS Chr4 17746419 C-A Hetero NON_SYNONYMOUS_CODING OsKitaake04g088900
SBS Chr4 29206175 T-C Homo INTRON
SBS Chr6 7872895 C-T Homo INTERGENIC
SBS Chr6 9666643 C-T Homo INTERGENIC
SBS Chr6 15478719 G-A Hetero INTERGENIC
SBS Chr6 19836266 G-A Hetero INTERGENIC
SBS Chr6 20562637 T-C Hetero INTERGENIC
SBS Chr6 20946413 C-T Hetero INTERGENIC
SBS Chr6 21542556 T-C Hetero INTERGENIC
SBS Chr6 25282769 G-A Hetero SPLICE_SITE_DONOR OsKitaake06g224100
SBS Chr7 209959 G-A Hetero INTRON
SBS Chr7 2876436 C-T Homo INTERGENIC
SBS Chr7 9660349 C-T Hetero INTERGENIC
SBS Chr7 9689958 T-C Hetero INTERGENIC
SBS Chr7 9899422 C-T Hetero INTERGENIC
SBS Chr7 20082307 T-C Hetero INTRON
SBS Chr8 4423458 C-T Hetero START_GAINED
SBS Chr8 7543889 T-C Homo INTERGENIC
SBS Chr8 8463820 G-C Hetero INTERGENIC
SBS Chr8 16761277 T-C Hetero INTERGENIC
SBS Chr8 26957365 G-T Homo INTERGENIC
SBS Chr9 15362216 G-T Homo INTERGENIC
SBS Chr9 22141097 C-A Homo INTERGENIC
SBS Chr10 2867650 T-G Hetero INTERGENIC
SBS Chr10 6126519 G-A Hetero INTERGENIC
SBS Chr10 6126520 G-A Hetero INTERGENIC
SBS Chr10 12702176 A-G Hetero INTERGENIC
SBS Chr10 12885517 C-T Hetero INTERGENIC
SBS Chr10 16323947 A-G Homo UTR_3_PRIME
SBS Chr11 20556741 T-A Hetero INTRON
SBS Chr12 9924805 G-C Homo INTERGENIC
SBS Chr12 11305046 C-G Homo INTERGENIC
SBS Chr12 16571913 C-A Homo INTERGENIC
SBS Chr12 16622898 G-A Homo INTERGENIC
SBS Chr12 17700549 C-T Homo INTERGENIC
SBS Chr12 20571261 T-C Hetero INTERGENIC

Deletions: 10

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr7 4874853 4874854 1
Deletion Chr12 14604400 14604401 1
Deletion Chr2 17536134 17536139 5
Deletion Chr4 17983084 17983090 6
Deletion Chr9 20053425 20053434 9
Deletion Chr11 20789595 20789605 10
Deletion Chr12 21016082 21016087 5
Deletion Chr7 23365905 23365906 1
Deletion Chr7 27050085 27050095 10
Deletion Chr1 34626483 34626492 9

Insertions: 5

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr3 23794776 23794779 2
Insertion Chr4 26617243 26617246 2
Insertion Chr9 14556879 14556892 12
Insertion Chr11 13627337 13627340 2
Insertion Chr6 16020336 16020338 1 OsKitaake06g154000

Inversions: 2

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Inversion Chr3 6519052 6842234 2
Inversion Chr3 6909266 7001388

Translocations: 6

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes

Translocation Chr10 1630794 Chr6 26022552 OsKitaake10g011600
Translocation Chr10 1630802 Chr6 26027329 OsKitaake10g011600
Translocation Chr3 10037953 Chr2 36689895
Translocation Chr3 10037959 Chr2 36690425
Translocation Chr4 30937012 Chr2 36690433
Translocation Chr4 30937941 Chr2 36689887

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	17925345	C-T	Homo	NON_SYNONYMOUS_CODING	OsKitaake01g181800
SBS	Chr1	27369506	C-T	Hetero	INTERGENIC
SBS	Chr2	11476635	C-T	Homo	INTERGENIC
SBS	Chr2	26683011	T-G	Hetero	INTERGENIC
SBS	Chr3	1928613	C-A	Hetero	NON_SYNONYMOUS_CODING	OsKitaake03g027600
SBS	Chr3	6525226	C-T	Hetero	INTERGENIC
SBS	Chr3	6792697	C-G	Hetero	INTERGENIC
SBS	Chr3	28827010	C-T	Hetero	INTERGENIC
SBS	Chr3	36243489	T-C	Hetero	INTERGENIC
SBS	Chr4	8752127	T-C	Hetero	UTR_3_PRIME
SBS	Chr4	9916519	C-G	Hetero	INTERGENIC
SBS	Chr4	10218421	C-T	Hetero	INTERGENIC
SBS	Chr4	11131560	G-T	Hetero	INTERGENIC
SBS	Chr4	13965682	A-C	Hetero	INTRON
SBS	Chr4	17744824	G-A	Hetero	NON_SYNONYMOUS_CODING	OsKitaake04g088900
SBS	Chr4	17746419	C-A	Hetero	NON_SYNONYMOUS_CODING	OsKitaake04g088900
SBS	Chr4	29206175	T-C	Homo	INTRON
SBS	Chr6	7872895	C-T	Homo	INTERGENIC
SBS	Chr6	9666643	C-T	Homo	INTERGENIC
SBS	Chr6	15478719	G-A	Hetero	INTERGENIC
SBS	Chr6	19836266	G-A	Hetero	INTERGENIC
SBS	Chr6	20562637	T-C	Hetero	INTERGENIC
SBS	Chr6	20946413	C-T	Hetero	INTERGENIC
SBS	Chr6	21542556	T-C	Hetero	INTERGENIC
SBS	Chr6	25282769	G-A	Hetero	SPLICE_SITE_DONOR	OsKitaake06g224100
SBS	Chr7	209959	G-A	Hetero	INTRON
SBS	Chr7	2876436	C-T	Homo	INTERGENIC
SBS	Chr7	9660349	C-T	Hetero	INTERGENIC
SBS	Chr7	9689958	T-C	Hetero	INTERGENIC
SBS	Chr7	9899422	C-T	Hetero	INTERGENIC
SBS	Chr7	20082307	T-C	Hetero	INTRON
SBS	Chr8	4423458	C-T	Hetero	START_GAINED
SBS	Chr8	7543889	T-C	Homo	INTERGENIC
SBS	Chr8	8463820	G-C	Hetero	INTERGENIC
SBS	Chr8	16761277	T-C	Hetero	INTERGENIC
SBS	Chr8	26957365	G-T	Homo	INTERGENIC
SBS	Chr9	15362216	G-T	Homo	INTERGENIC
SBS	Chr9	22141097	C-A	Homo	INTERGENIC
SBS	Chr10	2867650	T-G	Hetero	INTERGENIC
SBS	Chr10	6126519	G-A	Hetero	INTERGENIC
SBS	Chr10	6126520	G-A	Hetero	INTERGENIC
SBS	Chr10	12702176	A-G	Hetero	INTERGENIC
SBS	Chr10	12885517	C-T	Hetero	INTERGENIC
SBS	Chr10	16323947	A-G	Homo	UTR_3_PRIME
SBS	Chr11	20556741	T-A	Hetero	INTRON
SBS	Chr12	9924805	G-C	Homo	INTERGENIC
SBS	Chr12	11305046	C-G	Homo	INTERGENIC
SBS	Chr12	16571913	C-A	Homo	INTERGENIC
SBS	Chr12	16622898	G-A	Homo	INTERGENIC
SBS	Chr12	17700549	C-T	Homo	INTERGENIC
SBS	Chr12	20571261	T-C	Hetero	INTERGENIC

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr7	4874853	4874854	1
Deletion	Chr12	14604400	14604401	1
Deletion	Chr2	17536134	17536139	5
Deletion	Chr4	17983084	17983090	6
Deletion	Chr9	20053425	20053434	9
Deletion	Chr11	20789595	20789605	10
Deletion	Chr12	21016082	21016087	5
Deletion	Chr7	23365905	23365906	1
Deletion	Chr7	27050085	27050095	10
Deletion	Chr1	34626483	34626492	9

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr3	6519052	6842234	2
Inversion	Chr3	6909266	7001388

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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