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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
Mapping (Hover to Zoom-In)

Variant Information

Single base substitutions: 49

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	17562005	C-T	HOMO	NON_SYNONYMOUS_CODING	LOC_Os01g32080
SBS	Chr1	26646918	C-T	HET	INTERGENIC
SBS	Chr2	11385050	C-T	HOMO	INTERGENIC
SBS	Chr2	25964140	T-G	HET	INTERGENIC
SBS	Chr2	35465779	T-A	HOMO	INTERGENIC
SBS	Chr3	1838424	C-A	HET	NON_SYNONYMOUS_CODING	LOC_Os03g04030
SBS	Chr3	6619964	C-G	HET	INTERGENIC
SBS	Chr3	27732387	C-T	HET	INTERGENIC
SBS	Chr3	34903878	T-C	HET	INTERGENIC
SBS	Chr4	8032768	T-C	HET	INTERGENIC
SBS	Chr4	9519152	C-T	HET	NON_SYNONYMOUS_CODING	LOC_Os04g17400
SBS	Chr4	10452124	G-T	HET	INTERGENIC
SBS	Chr4	12994126	A-C	HET	UTR_3_PRIME
SBS	Chr4	16949636	G-A	HET	NON_SYNONYMOUS_CODING	LOC_Os04g28620
SBS	Chr4	16951232	C-A	HET	NON_SYNONYMOUS_CODING	LOC_Os04g28620
SBS	Chr4	27920780	T-C	HOMO	INTRON
SBS	Chr6	7708403	C-T	HOMO	INTERGENIC
SBS	Chr6	9431991	C-T	HOMO	INTERGENIC
SBS	Chr6	15171345	G-A	HET	INTERGENIC
SBS	Chr6	20211010	G-A	HET	INTERGENIC
SBS	Chr6	20975051	T-C	HET	INTERGENIC
SBS	Chr6	21358184	C-T	HET	INTERGENIC
SBS	Chr6	21933399	T-C	HET	INTERGENIC
SBS	Chr6	25683013	G-A	HET	INTERGENIC
SBS	Chr7	141403	G-A	HET	INTRON
SBS	Chr7	2874500	C-T	HOMO	INTERGENIC
SBS	Chr7	9731790	C-T	HET	SYNONYMOUS_CODING
SBS	Chr7	9761399	T-C	HET	INTRON
SBS	Chr7	9970617	C-T	HET	INTERGENIC
SBS	Chr7	20150894	T-C	HET	INTRON
SBS	Chr8	4351613	C-T	HET	INTERGENIC
SBS	Chr8	7322360	T-C	HOMO	INTERGENIC
SBS	Chr8	8242220	G-C	HET	INTERGENIC
SBS	Chr8	16367810	T-C	HET	INTERGENIC
SBS	Chr8	26078573	G-T	HOMO	INTERGENIC
SBS	Chr9	15668779	G-T	HOMO	INTERGENIC
SBS	Chr9	22324772	C-A	HOMO	INTERGENIC
SBS	Chr10	2804572	T-G	HET	NON_SYNONYMOUS_CODING	LOC_Os10g05620
SBS	Chr10	5798945	G-A	HET	INTERGENIC
SBS	Chr10	5798946	G-A	HET	INTERGENIC
SBS	Chr10	12026396	A-G	HET	INTERGENIC
SBS	Chr10	15629491	A-G	HOMO	UTR_3_PRIME
SBS	Chr11	20267179	T-A	HET	INTRON
SBS	Chr12	10336243	G-C	HOMO	INTERGENIC
SBS	Chr12	11689428	C-G	HET	INTERGENIC
SBS	Chr12	16865620	C-A	HOMO	INTERGENIC
SBS	Chr12	16916489	G-A	HOMO	INTERGENIC
SBS	Chr12	17967926	C-T	HOMO	INTERGENIC
SBS	Chr12	21084237	T-C	HET	SYNONYMOUS_CODING

Deletions: 19

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Deletion	Chr5	127386	127392	6
Deletion	Chr10	1071145	1071153	8
Deletion	Chr5	1927875	1927886	11
Deletion	Chr10	4684144	4684159	15
Deletion	Chr7	4938921	4938922	1
Deletion	Chr9	4984161	4985051	890
Deletion	Chr8	9620997	9621009	12
Deletion	Chr12	14933940	14933941	1	LOC_Os12g25760
Deletion	Chr7	16941130	16941131	1
Deletion	Chr4	17187948	17187954	6	LOC_Os04g29010
Deletion	Chr2	17347242	17347247	5
Deletion	Chr9	20282402	20282411	9
Deletion	Chr11	20498847	20498857	10	LOC_Os11g34970
Deletion	Chr12	21500869	21500874	5
Deletion	Chr7	23163132	23163154	22
Deletion	Chr7	23389574	23389575	1	LOC_Os07g39010
Deletion	Chr7	25845427	25845448	21	LOC_Os07g43130
Deletion	Chr6	26392082	26396906	4824	LOC_Os06g43830
Deletion	Chr7	27091843	27091853	10	LOC_Os07g45410

Insertions: 9

Variant Type	Chromosome	Start	End	Size (bp)
Insertion	Chr3	23126868	23126869	2
Insertion	Chr4	25364162	25364163	2
Insertion	Chr9	14853390	14853401	12
Insertion	Chr3	6221716	6221717	2
Insertion	Chr3	12521450	12521450	1
Insertion	Chr6	7354858	7354858	1
Insertion	Chr6	7561931	7561931	1
Insertion	Chr8	5267627	5267627	1
Insertion	Chr11	22614828	22614829	2

Inversions: 2

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr3	6346388	6665950	LOC_Os03g12570
Inversion	Chr3	6733080	6825236

Translocations: 6

Variant Type	Chromosome	Position 1	Chromosome	Position 2	Number of Genes
Translocation	Chr10	1563370	Chr6	26392115	LOC_Os10g03620
Translocation	Chr10	1563378	Chr6	26396940	LOC_Os10g03620
Translocation	Chr3	9910289	Chr2	35465719
Translocation	Chr4	16363770	Chr1	23524840	LOC_Os04g27680
Translocation	Chr4	29639523	Chr2	35466257
Translocation	Chr4	29640450	Chr2	35465712

Tandem duplications: 1

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Tandem Duplication	Chr3	6665974	6665974	0	LOC_Os03g12570

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