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Mutant Information

Mutant Name	FN1660-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN1660-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: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: 42

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	19062047	T-C	HET	INTERGENIC
SBS	Chr1	40236435	C-G	HET	NON_SYNONYMOUS_CODING	LOC_Os01g69230
SBS	Chr10	13502029	C-A	HET	NON_SYNONYMOUS_CODING	LOC_Os10g26070
SBS	Chr11	11493372	C-T	HET	SYNONYMOUS_CODING
SBS	Chr11	13346466	G-T	HET	NON_SYNONYMOUS_CODING	LOC_Os11g23180
SBS	Chr11	13696896	A-T	HET	INTRON
SBS	Chr11	21011729	A-G	HET	NON_SYNONYMOUS_CODING	LOC_Os11g35800
SBS	Chr11	5645707	A-T	HET	UTR_3_PRIME
SBS	Chr12	10762243	C-A	HET	INTRON
SBS	Chr12	14304436	A-T	Homo	INTERGENIC
SBS	Chr12	23163029	A-G	HET	INTRON
SBS	Chr12	9056295	C-A	HET	NON_SYNONYMOUS_CODING	LOC_Os12g15910
SBS	Chr2	14744257	C-T	HET	INTERGENIC
SBS	Chr2	15995611	C-T	Homo	INTERGENIC
SBS	Chr3	11914889	G-A	HET	INTERGENIC
SBS	Chr3	22806477	C-T	HET	INTERGENIC
SBS	Chr3	29171496	T-C	HET	NON_SYNONYMOUS_CODING	LOC_Os03g51030
SBS	Chr3	3151860	G-C	HET	NON_SYNONYMOUS_CODING	LOC_Os03g06290
SBS	Chr3	9416377	G-C	HET	INTERGENIC
SBS	Chr4	13136832	A-G	HET	INTERGENIC
SBS	Chr4	16618361	C-A	HET	INTERGENIC
SBS	Chr4	16618362	C-T	HET	INTERGENIC
SBS	Chr4	21553656	A-T	HET	INTRON
SBS	Chr4	23800004	G-A	HET	INTERGENIC
SBS	Chr4	23908116	T-A	HET	INTERGENIC
SBS	Chr4	25834734	C-T	HET	UTR_3_PRIME
SBS	Chr4	28824811	C-T	HET	INTERGENIC
SBS	Chr4	4664314	C-T	HET	INTERGENIC
SBS	Chr5	2987508	C-A	HET	INTRON
SBS	Chr6	1216143	C-T	HET	INTERGENIC
SBS	Chr6	15154401	T-C	HET	INTERGENIC
SBS	Chr6	21778151	A-G	HET	INTRON
SBS	Chr6	26501757	A-G	Homo	INTERGENIC
SBS	Chr6	5434705	G-T	Homo	INTERGENIC
SBS	Chr6	5888046	C-T	HET	INTERGENIC
SBS	Chr7	21461588	T-A	Homo	INTERGENIC
SBS	Chr7	26938426	G-A	HET	INTERGENIC
SBS	Chr8	15808409	C-T	HET	NON_SYNONYMOUS_CODING	LOC_Os08g25980
SBS	Chr8	24087856	G-A	Homo	INTERGENIC
SBS	Chr8	24087857	C-A	Homo	INTERGENIC
SBS	Chr8	5889593	T-C	HET	INTRON
SBS	Chr9	17975533	T-G	HET	INTERGENIC

Deletions: 34

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Deletion	Chr4	352743	352747	4
Deletion	Chr8	465264	465404	140
Deletion	Chr11	934743	934744	1
Deletion	Chr1	1375553	1375564	11	LOC_Os01g03420
Deletion	Chr9	3560610	3560633	23	LOC_Os09g07260
Deletion	Chr1	5554798	5583469	28671	2
Deletion	Chr2	5805641	5805642	1
Deletion	Chr1	6521132	6549964	28832	8
Deletion	Chr9	8234866	8235001	135	LOC_Os09g13980
Deletion	Chr2	8693974	8693976	2
Deletion	Chr7	8962845	8962847	2
Deletion	Chr6	9495787	9495788	1
Deletion	Chr12	9883714	9883733	19	LOC_Os12g17270
Deletion	Chr11	10193082	10193083	1
Deletion	Chr2	13112086	13112088	2
Deletion	Chr12	14565436	14565437	1
Deletion	Chr4	15467932	15468095	163
Deletion	Chr1	15689146	15689147	1
Deletion	Chr5	15904703	15904704	1
Deletion	Chr9	16951638	16951639	1
Deletion	Chr9	17151533	17151534	1
Deletion	Chr12	17501400	17501411	11
Deletion	Chr12	19633468	19633469	1
Deletion	Chr8	20202193	20202207	14
Deletion	Chr9	20558206	20558207	1	LOC_Os09g35740
Deletion	Chr11	23874735	23874739	4	LOC_Os11g40040
Deletion	Chr12	24302505	24302507	2
Deletion	Chr12	24361140	24361153	13
Deletion	Chr2	25200159	25200160	1
Deletion	Chr2	26043189	26043190	1
Deletion	Chr7	26072016	26072017	1
Deletion	Chr1	26262240	26262248	8
Deletion	Chr11	28439782	28439943	161
Deletion	Chr2	35847890	35847892	2

Insertions: 8

Variant Type	Chromosome	Start	End	Size (bp)
Insertion	Chr1	13350433	13350453	21
Insertion	Chr1	22421619	22421619	1
Insertion	Chr1	5031632	5031633	2
Insertion	Chr4	24926462	24926463	2
Insertion	Chr5	3125273	3125280	8
Insertion	Chr6	2880079	2880079	1
Insertion	Chr7	15986382	15986385	4
Insertion	Chr9	17298029	17298029	1

Inversions: 2

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr8	18655811	19268779
Inversion	Chr4	30373114	30616851	LOC_Os04g51260

Translocations: 3

Variant Type	Chromosome	Position 1	Chromosome	Position 2	Number of Genes
Translocation	Chr9	488389	Chr6	11179783	2
Translocation	Chr9	488420	Chr6	11179452	LOC_Os09g01680
Translocation	Chr12	27018183	Chr7	4769691	LOC_Os07g09130

Tandem duplications: 1

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Tandem Duplication	Chr1	6535298	6535298	0	LOC_Os01g12000

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