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Mutant Information

Mutant Name	W246-5-1 [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download W246-5-1 Alignment File
Seed Availability	No
Phenotype	TO:0000014 (Panicle Weight) = Very Low (below 24% compare to WT) TO:0000207 (Plant height) = Normal (Between 75% and 125%) TO:0000445 (Seed Number) = Low (Between 25% and 74%) TO:0000639 (Seed fertility) = Low (Between 25% and 74%) For more information, please see this phenotype file
Mapping (Hover to Zoom-In)

Variant Information

Single base substitutions: 43

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	2005649	C-A	HOMO	INTERGENIC
SBS	Chr1	14047336	A-T	HOMO	INTERGENIC
SBS	Chr1	17317570	G-A	HOMO	INTRON
SBS	Chr1	21079068	C-A	HOMO	INTRON
SBS	Chr1	23860439	A-T	HOMO	INTRON
SBS	Chr1	23860440	G-T	HOMO	INTRON
SBS	Chr2	1252284	G-C	HET	INTERGENIC
SBS	Chr2	30693973	C-T	HET	INTERGENIC
SBS	Chr2	34717979	C-T	HOMO	INTERGENIC
SBS	Chr3	6500508	A-C	HOMO	INTERGENIC
SBS	Chr3	13638670	G-T	HOMO	INTERGENIC
SBS	Chr3	13638671	C-T	HOMO	INTERGENIC
SBS	Chr3	26478962	T-C	HOMO	INTERGENIC
SBS	Chr4	61485	C-T	HET	SYNONYMOUS_CODING
SBS	Chr4	20178665	A-G	HET	INTERGENIC
SBS	Chr4	22633583	G-T	HET	INTERGENIC
SBS	Chr5	380313	C-T	HET	INTERGENIC
SBS	Chr5	1511906	T-A	HET	INTERGENIC
SBS	Chr5	5576495	C-G	HET	NON_SYNONYMOUS_CODING	LOC_Os05g10250
SBS	Chr5	8312171	G-A	HOMO	INTERGENIC
SBS	Chr6	29159055	C-T	HOMO	INTERGENIC
SBS	Chr7	10608673	C-T	HOMO	INTERGENIC
SBS	Chr8	9309255	T-G	HET	NON_SYNONYMOUS_CODING	LOC_Os08g15310
SBS	Chr8	17195809	A-G	HET	UTR_3_PRIME
SBS	Chr8	23329668	C-T	HOMO	INTERGENIC
SBS	Chr8	27323581	T-A	HET	INTERGENIC
SBS	Chr8	27323582	C-A	HET	INTERGENIC
SBS	Chr8	27323583	T-A	HET	INTERGENIC
SBS	Chr9	6029287	G-T	HOMO	INTERGENIC
SBS	Chr9	21419153	G-A	HOMO	INTERGENIC
SBS	Chr9	22395327	T-A	HET	INTERGENIC
SBS	Chr11	10883642	G-T	HOMO	INTERGENIC
SBS	Chr11	18168616	C-G	HOMO	INTERGENIC
SBS	Chr11	24810994	T-A	HOMO	INTERGENIC
SBS	Chr12	2880214	C-T	HOMO	INTERGENIC
SBS	Chr12	3152475	A-G	HOMO	INTERGENIC
SBS	Chr12	5376117	C-T	HET	INTERGENIC
SBS	Chr12	15992327	G-C	HOMO	INTERGENIC
SBS	Chr12	16073253	C-T	HOMO	INTERGENIC
SBS	Chr12	16073255	A-T	HOMO	INTERGENIC
SBS	Chr12	16073258	C-T	HOMO	INTERGENIC
SBS	Chr12	17015720	T-C	HET	NON_SYNONYMOUS_CODING	LOC_Os12g28780
SBS	Chr12	24429674	A-C	HET	NON_SYNONYMOUS_CODING	LOC_Os12g39590

Deletions: 22

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Deletion	Chr8	58436	62929	4493	LOC_Os08g01080
Deletion	Chr8	592233	592238	5
Deletion	Chr9	1688445	1688447	2	LOC_Os09g03420
Deletion	Chr9	3000114	3000115	1
Deletion	Chr10	10063918	10063919	1
Deletion	Chr10	10505626	10505645	19
Deletion	Chr4	11374740	11374742	2
Deletion	Chr3	12491713	12491714	1
Deletion	Chr5	15561191	15561192	1
Deletion	Chr12	15884700	15884714	14
Deletion	Chr6	16641432	16641443	11
Deletion	Chr5	17829070	17829071	1
Deletion	Chr10	17832498	17832516	18
Deletion	Chr12	18829846	18829859	13
Deletion	Chr6	20016654	20016655	1
Deletion	Chr6	20388678	20388679	1
Deletion	Chr6	21217147	21217162	15	LOC_Os06g36220
Deletion	Chr11	21677895	21677896	1
Deletion	Chr8	22647001	22659000	12000	3
Deletion	Chr8	27501005	27501022	17	LOC_Os08g43470
Deletion	Chr4	31409347	31409353	6
Deletion	Chr1	42589895	42609501	19606	3

Insertions: 6

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Insertion	Chr12	3494172	3494172	1
Insertion	Chr5	6402287	6402290	4
Insertion	Chr4	19690674	19690675	2	LOC_Os04g32670
Insertion	Chr6	7932742	7932742	1
Insertion	Chr7	23080855	23080855	1
Insertion	Chr8	18494296	18494296	1

Inversions: 10

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr12	1675560	2648766	LOC_Os12g05740
Inversion	Chr11	10823954	11165736	LOC_Os11g19420
Inversion	Chr1	12644998	14455138
Inversion	Chr1	12645016	14455150
Inversion	Chr12	14830482	15153459	2
Inversion	Chr12	15153473	16034554	LOC_Os12g26080
Inversion	Chr12	15510465	16034553	LOC_Os12g26540
Inversion	Chr8	15928429	16353204
Inversion	Chr1	42329617	42765390	LOC_Os01g72980
Inversion	Chr1	42334784	42653577	2

Translocations: 8

Variant Type	Chromosome	Position 1	Chromosome	Position 2	Number of Genes
Translocation	Chr6	5584937	Chr1	42590421
Translocation	Chr12	14093911	Chr4	14630935
Translocation	Chr12	14830484	Chr6	5579610	2
Translocation	Chr12	15510483	Chr1	42589896	2
Translocation	Chr8	22135557	Chr1	1232743	LOC_Os01g03160
Translocation	Chr3	28717930	Chr2	6171088
Translocation	Chr4	30769606	Chr1	42653573	2
Translocation	Chr4	30769685	Chr1	42652598	2

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