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Mutant Information

Mutant Name	FN1396-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN1396-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
Mapping (Hover to Zoom-In)

Variant Information

Single base substitutions: 30

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr10	15582704	A-G	HET	INTRON
SBS	Chr10	21262167	A-T	HOMO	INTERGENIC
SBS	Chr10	4825944	T-C	HOMO	NON_SYNONYMOUS_CODING	LOC_Os10g08920
SBS	Chr10	9013621	C-A	HET	INTERGENIC
SBS	Chr11	24237317	T-A	HOMO	INTERGENIC
SBS	Chr12	22945448	C-T	HET	INTERGENIC
SBS	Chr12	23171758	G-A	HOMO	UTR_5_PRIME
SBS	Chr12	23171764	C-A	HOMO	START_GAINED	LOC_Os12g37740
SBS	Chr12	5009800	G-A	HET	INTERGENIC
SBS	Chr2	10138390	C-G	HOMO	INTRON
SBS	Chr2	16963631	A-G	HOMO	INTRON
SBS	Chr2	6351478	A-G	HET	INTERGENIC
SBS	Chr3	11759595	G-T	HOMO	INTERGENIC
SBS	Chr3	14413091	C-T	HOMO	INTERGENIC
SBS	Chr3	31832364	T-A	HET	INTERGENIC
SBS	Chr3	4438084	C-A	HET	UTR_3_PRIME
SBS	Chr3	7129959	C-T	HOMO	INTRON
SBS	Chr4	12634400	A-G	HOMO	INTRON
SBS	Chr4	26833439	T-A	HOMO	INTERGENIC
SBS	Chr4	26833440	T-A	HOMO	INTERGENIC
SBS	Chr4	8995382	C-T	HET	NON_SYNONYMOUS_CODING	LOC_Os04g16540
SBS	Chr5	1965199	A-G	HOMO	INTERGENIC
SBS	Chr5	24448941	C-A	HOMO	INTERGENIC
SBS	Chr5	24867098	A-G	HET	INTERGENIC
SBS	Chr5	26767558	G-A	HOMO	INTERGENIC
SBS	Chr6	24126824	A-G	HET	INTERGENIC
SBS	Chr6	28679223	T-A	HET	INTERGENIC
SBS	Chr8	1544448	C-T	HOMO	NON_SYNONYMOUS_CODING	LOC_Os08g03330
SBS	Chr9	3175326	T-C	HET	INTERGENIC
SBS	Chr9	5862020	G-A	HET	INTERGENIC

Deletions: 19

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Deletion	Chr4	4587864	4587865	1
Deletion	Chr9	7696001	7744000	48000	7
Deletion	Chr7	8984896	8984897	1
Deletion	Chr11	9412195	9412196	1
Deletion	Chr7	11715943	11715944	1
Deletion	Chr3	11727713	11727740	27	LOC_Os03g20720
Deletion	Chr1	12069711	12069724	13
Deletion	Chr7	15975191	15975193	2
Deletion	Chr11	16006001	16238000	232000	37
Deletion	Chr7	16131043	16131044	1	LOC_Os07g27620
Deletion	Chr3	19027930	19027931	1	LOC_Os03g33260
Deletion	Chr4	20595955	20596005	50	LOC_Os04g34010
Deletion	Chr10	21963548	21963549	1
Deletion	Chr12	24168987	24172680	3693	LOC_Os12g39270
Deletion	Chr4	24776284	24776292	8
Deletion	Chr4	30765500	30765501	1
Deletion	Chr1	30919748	30919749	1
Deletion	Chr1	37741034	37741047	13	LOC_Os01g65010
Deletion	Chr1	38963262	38963267	5	LOC_Os01g67120

Insertions: 5

Variant Type	Chromosome	Start	End	Size (bp)
Insertion	Chr2	24179472	24179473	2
Insertion	Chr3	32604039	32604039	1
Insertion	Chr6	17470688	17470688	1
Insertion	Chr8	26442291	26442292	2
Insertion	Chr9	21159465	21159466	2

Inversions: 6

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr8	10886879	11877122	LOC_Os08g19830
Inversion	Chr8	10886899	11877123	LOC_Os08g19830
Inversion	Chr7	12458671	13590616	LOC_Os07g23990
Inversion	Chr7	13590612	14504522	LOC_Os07g23990
Inversion	Chr7	14504524	14637515
Inversion	Chr7	22650391	24289584	LOC_Os07g37760

Translocations: 1

Variant Type	Chromosome	Position 1	Chromosome	Position 2	Number of Genes
Translocation	Chr9	6281814	Chr3	31100519

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