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Mutant Information

Mutant Name	FN3039-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN3039-S Alignment File
Seed Availability	Yes [Order Seeds]
Phenotype	TO:0000430 (Germination Rate) = Very Low (Below 24%) For more information, please see this phenotype file
Mapping (Hover to Zoom-In)

Variant Information

Single base substitutions: 31

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	11932646	A-G	HET
SBS	Chr1	18713849	G-A	HET
SBS	Chr10	4273769	G-A	HET
SBS	Chr10	4734594	T-C	HET
SBS	Chr11	18223290	G-A	HET
SBS	Chr11	4190645	G-A	Homo
SBS	Chr12	7550816	T-A	HET
SBS	Chr2	17223059	C-T	HET
SBS	Chr2	21368267	G-A	HET
SBS	Chr3	18788271	G-A	HET
SBS	Chr3	22170706	T-C	HET
SBS	Chr4	214886	A-G	Homo
SBS	Chr4	2467999	T-G	Homo
SBS	Chr4	9927598	C-T	Homo
SBS	Chr5	134203	A-T	HET
SBS	Chr5	134207	C-T	HET
SBS	Chr5	5826522	T-C	HET
SBS	Chr5	6045777	C-A	HET
SBS	Chr6	14356375	G-A	HET
SBS	Chr6	14860784	C-T	HET	NON_SYNONYMOUS_CODING	LOC_Os06g25370
SBS	Chr6	19291115	G-T	Homo
SBS	Chr6	22189191	G-C	Homo
SBS	Chr7	19475613	A-G	HET
SBS	Chr8	15726741	G-A	HET
SBS	Chr8	27884637	G-A	HET	NON_SYNONYMOUS_CODING	LOC_Os08g44300
SBS	Chr8	8422184	A-G	HET
SBS	Chr9	1086431	C-T	HET
SBS	Chr9	1219773	C-T	HET
SBS	Chr9	15872099	A-C	Homo
SBS	Chr9	4077282	T-A	HET
SBS	Chr9	9710730	C-T	HET	NON_SYNONYMOUS_CODING	LOC_Os09g15890

Deletions: 12

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Deletion	Chr5	1901762	1901763	1
Deletion	Chr5	4958001	4992000	33999	5
Deletion	Chr1	7927285	7927318	33	LOC_Os01g14130
Deletion	Chr5	10588489	10588490	1
Deletion	Chr2	11142922	11142923	1	LOC_Os02g19100
Deletion	Chr2	11490952	11490957	5
Deletion	Chr7	12924528	12924532	4
Deletion	Chr4	16050701	16050705	4
Deletion	Chr5	17201562	17201563	1
Deletion	Chr6	21771802	21771807	5
Deletion	Chr12	21842515	21842731	216
Deletion	Chr3	24462905	24462907	2

Insertions: 2

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Insertion	Chr7	22054665	22054666	2
Insertion	Chr8	25824153	25824155	3

Inversions: 4

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr5	4960599	5617675	LOC_Os05g08960
Inversion	Chr5	4989513	5617682
Inversion	Chr11	24984739	25190324
Inversion	Chr11	24984742	25190335

Translocations: 7

Variant Type	Chromosome	Position 1	Chromosome	Position 2	Number of Genes
Translocation	Chr11	8063948	Chr10	4751593	LOC_Os11g14360
Translocation	Chr11	9676191	Chr3	19441550	2
Translocation	Chr6	12092544	Chr5	110102
Translocation	Chr11	18328330	Chr5	24765051	2
Translocation	Chr11	18329012	Chr5	24765068	2
Translocation	Chr11	21846360	Chr8	23507491
Translocation	Chr5	23913026	Chr4	3658238

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