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Mutant Information

Mutant Name	N1-169-5 [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download N1-169-5 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: 9

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	28624542	A-T	Homo	INTERGENIC
SBS	Chr3	30842059	T-A	Homo	INTERGENIC
SBS	Chr3	34180630	C-T	HET	INTERGENIC
SBS	Chr3	34180653	G-C	HET	INTERGENIC
SBS	Chr3	34180679	A-G	HET	INTERGENIC
SBS	Chr4	30362164	C-A	Homo	UTR_3_PRIME
SBS	Chr5	27454544	G-A	Homo	INTRON
SBS	Chr8	506537	C-T	HET	INTERGENIC
SBS	Chr11	25681971	G-A	Homo	INTRON

Deletions: 17

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Deletion	Chr3	9546101	9546166	65	LOC_Os03g17164
Deletion	Chr12	20094883	20094887	4	LOC_Os12g33220
Deletion	Chr6	20976938	20976948	10
Deletion	Chr9	22104001	22334000	230000	51
Deletion	Chr6	22278456	22278457	1
Deletion	Chr9	22341001	22393000	52000	11
Deletion	Chr3	22517148	22517149	1
Deletion	Chr5	23117705	23117715	10
Deletion	Chr8	25104527	25104542	15
Deletion	Chr8	25616375	25616556	181
Deletion	Chr2	27833483	27833484	1
Deletion	Chr3	28492066	28492067	1
Deletion	Chr5	29375434	29375458	24
Deletion	Chr2	32041323	32041331	8
Deletion	Chr3	34177001	34186000	9000
Deletion	Chr3	34179264	34179265	1
Deletion	Chr1	39117699	39117705	6

Insertions: 2

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Insertion	Chr11	16764607	16764608	2
Insertion	Chr8	27506747	27506747	1

Inversions: 7

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr8	4042473	4124579
Inversion	Chr2	7261134	7495409	2
Inversion	Chr2	7495634	7578370	2
Inversion	Chr12	20862332	22212773	LOC_Os12g34440
Inversion	Chr1	23159766	24946752	LOC_Os01g43550
Inversion	Chr1	32933790	33211643	LOC_Os01g57480
Inversion	Chr1	33005449	33211643	2

Translocations: 4

Variant Type	Chromosome	Position 1	Chromosome	Position 2	Number of Genes
Translocation	Chr9	6014109	Chr1	39128731
Translocation	Chr9	22393238	Chr4	25255377	LOC_Os04g42700
Translocation	Chr3	34145107	Chr1	32933774	LOC_Os03g60030
Translocation	Chr3	34177151	Chr1	33005460	LOC_Os01g57110

Tandem duplications: 1

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Tandem Duplication	Chr3	36136483	36140436	3953