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Mutant Information

Mutant Name	FN1340-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN1340-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) = Low (Between 25% and 74%) 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: 34

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	5964114	T-C	HET	SYNONYMOUS_CODING
SBS	Chr1	7824111	C-T	HET	INTRON
SBS	Chr1	14726756	A-T	HET	STOP_GAINED	LOC_Os01g25970
SBS	Chr1	14954797	G-A	HOMO	INTERGENIC
SBS	Chr1	37911896	G-A	HOMO	INTERGENIC
SBS	Chr2	19023097	A-C	HOMO	UTR_3_PRIME
SBS	Chr3	502103	C-T	HET	INTERGENIC
SBS	Chr3	3058254	A-C	HET	INTRON
SBS	Chr3	5024961	G-A	HET	INTERGENIC
SBS	Chr3	24815524	T-A	HET	INTRON
SBS	Chr3	36023330	G-A	HET	NON_SYNONYMOUS_CODING	LOC_Os03g63790
SBS	Chr4	10132283	A-T	HET	NON_SYNONYMOUS_CODING	LOC_Os04g18360
SBS	Chr4	15290461	C-T	HET	INTERGENIC
SBS	Chr4	27725275	C-A	HOMO	INTERGENIC
SBS	Chr5	3682734	G-A	HET	INTRON
SBS	Chr5	11576164	T-A	HOMO	NON_SYNONYMOUS_CODING	LOC_Os05g19870
SBS	Chr6	5770035	T-C	HET	INTERGENIC
SBS	Chr6	11260293	C-T	HET	INTERGENIC
SBS	Chr6	19691116	C-A	HET	INTERGENIC
SBS	Chr7	2458484	T-G	HOMO	UTR_3_PRIME
SBS	Chr7	15473248	A-G	HOMO	NON_SYNONYMOUS_CODING	LOC_Os07g26780
SBS	Chr7	15473249	C-G	HOMO	SYNONYMOUS_CODING
SBS	Chr7	15477806	T-C	HOMO	INTERGENIC
SBS	Chr8	5237860	C-T	HET	INTERGENIC
SBS	Chr8	23166311	C-T	HET	INTERGENIC
SBS	Chr9	1589119	A-T	HET	NON_SYNONYMOUS_CODING	LOC_Os09g03300
SBS	Chr9	4062920	T-A	HET	INTERGENIC
SBS	Chr10	750397	G-T	HET	INTRON
SBS	Chr10	4221771	A-G	HET	INTERGENIC
SBS	Chr11	9674140	G-A	HET	INTERGENIC
SBS	Chr11	15099185	C-T	HET	INTERGENIC
SBS	Chr11	18164729	T-C	HET	INTERGENIC
SBS	Chr11	22805918	G-A	HOMO	INTERGENIC
SBS	Chr12	24164062	T-C	HOMO	NON_SYNONYMOUS_CODING	LOC_Os12g39260

Deletions: 30

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Deletion	Chr7	149504	149505	1
Deletion	Chr3	502107	502111	4
Deletion	Chr4	593247	593248	1
Deletion	Chr8	1556824	1556828	4
Deletion	Chr9	1572989	1572995	6	LOC_Os09g03270
Deletion	Chr3	3493182	3493184	2
Deletion	Chr4	3836146	3836147	1
Deletion	Chr9	4062990	4063002	12
Deletion	Chr11	5283434	5283854	420	LOC_Os11g09864
Deletion	Chr2	5527731	5527734	3
Deletion	Chr9	5896160	5896161	1
Deletion	Chr3	7355950	7355962	12
Deletion	Chr9	9030500	9030502	2
Deletion	Chr4	12284001	12406000	122000	19
Deletion	Chr4	12661607	12661614	7
Deletion	Chr2	13738184	13738185	1	LOC_Os02g23821
Deletion	Chr5	15088355	15088384	29
Deletion	Chr10	15135031	15135033	2	LOC_Os10g29040
Deletion	Chr12	15167001	15197000	30000	3
Deletion	Chr12	15202001	15267000	65000	6
Deletion	Chr7	15473246	15473312	66	LOC_Os07g26780
Deletion	Chr9	17327415	17327416	1	2
Deletion	Chr8	17381212	17381216	4
Deletion	Chr3	18003541	18003542	1
Deletion	Chr8	20569943	20569947	4
Deletion	Chr7	21303615	21303617	2
Deletion	Chr12	22476664	22476665	1
Deletion	Chr3	22880122	23098055	217933	27
Deletion	Chr5	24270934	24270935	1
Deletion	Chr1	32226608	32226609	1

Insertions: 6

Variant Type	Chromosome	Start	End	Size (bp)
Insertion	Chr4	11899988	11899988	1
Insertion	Chr7	4213510	4213511	2
Insertion	Chr3	28347247	28347247	1
Insertion	Chr6	27130855	27130855	1
Insertion	Chr7	28354245	28354246	2
Insertion	Chr12	17664451	17664451	1

Inversions: 4

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr8	7784390	7856778	LOC_Os08g13210
Inversion	Chr8	7784405	7856785	LOC_Os08g13210
Inversion	Chr1	8748919	8822073	LOC_Os01g15680
Inversion	Chr4	11921176	12283997

Translocations: 3

Variant Type	Chromosome	Position 1	Chromosome	Position 2	Number of Genes
Translocation	Chr5	17232399	Chr3	20467841	2
Translocation	Chr3	22880751	Chr2	18517332	LOC_Os02g31000
Translocation	Chr11	23663222	Chr6	11605656

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