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Mutant Information

Mutant Name	W475-4-2 [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download W475-4-2 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: 26

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	8514905	G-A	HOMO	NON_SYNONYMOUS_CODING	LOC_Os01g15180
SBS	Chr1	32570228	A-G	HOMO	INTERGENIC
SBS	Chr1	34161355	A-G	HOMO	INTERGENIC
SBS	Chr2	16089508	C-T	HOMO	INTRON
SBS	Chr2	23668846	C-T	HOMO	INTERGENIC
SBS	Chr3	19331810	T-A	HOMO	NON_SYNONYMOUS_CODING	LOC_Os03g33828
SBS	Chr4	5714922	G-A	HET	INTERGENIC
SBS	Chr4	10395534	G-A	HET	SYNONYMOUS_CODING
SBS	Chr4	30897236	T-C	HOMO	INTRON
SBS	Chr4	31425606	A-G	HOMO	INTERGENIC
SBS	Chr4	31425608	T-A	HOMO	INTERGENIC
SBS	Chr4	34296862	G-A	HOMO	INTERGENIC
SBS	Chr4	35358065	A-T	HOMO	INTERGENIC
SBS	Chr5	17063378	C-T	HOMO	INTERGENIC
SBS	Chr5	17232743	G-A	HOMO	NON_SYNONYMOUS_CODING	LOC_Os05g29780
SBS	Chr5	26935163	T-A	HET	INTRON
SBS	Chr6	8765906	G-A	HOMO	INTERGENIC
SBS	Chr6	15858673	A-T	HOMO	SYNONYMOUS_CODING
SBS	Chr6	22687389	T-C	HOMO	INTERGENIC
SBS	Chr7	25799362	G-A	HOMO	INTRON
SBS	Chr9	1330091	C-T	HET	INTERGENIC
SBS	Chr9	21892690	G-T	HET	SYNONYMOUS_CODING
SBS	Chr10	19856616	T-C	HOMO	INTERGENIC
SBS	Chr11	20254800	C-T	HET	INTERGENIC
SBS	Chr11	28913097	T-C	HOMO	INTERGENIC
SBS	Chr12	12365235	C-T	HOMO	UTR_3_PRIME

Deletions: 13

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Deletion	Chr1	2000495	2000496	1
Deletion	Chr4	7082001	7533000	451000	61
Deletion	Chr4	7539001	7698000	159000	29
Deletion	Chr6	12844099	12844109	10
Deletion	Chr9	13133868	13133869	1
Deletion	Chr4	16750839	16750844	5
Deletion	Chr5	26800148	26800159	11	LOC_Os05g46200
Deletion	Chr6	27126757	27126777	20
Deletion	Chr8	27682136	27682139	3
Deletion	Chr8	27887224	27887225	1
Deletion	Chr11	28732227	28732232	5
Deletion	Chr4	34033520	34033524	4	LOC_Os04g57110
Deletion	Chr1	36087332	36087338	6

Insertions: 6

Variant Type	Chromosome	Start	End	Size (bp)
Insertion	Chr4	26135799	26135801	3
Insertion	Chr5	17289595	17289598	4
Insertion	Chr1	3341686	3341687	2
Insertion	Chr2	8950121	8950122	2
Insertion	Chr12	14350746	14350746	1
Insertion	Chr4	16446310	16446310	1

Inversions: 2

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr5	4790836	5384617
Inversion	Chr5	7753800	7813644

No Translocation

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