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Mutant Information

Mutant Name	FN343-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN343-S Alignment File
Seed Availability	Yes [Order Seeds]
Phenotype	TO:0000014 (Panicle Weight) = Normal (Between 75% and 125%) TO:0000207 (Plant height) = Normal (Between 75% and 125%) TO:0000445 (Seed Number) = Normal (Between 75% and 125%) TO:0000430 (Germination Rate) = Low (Between 25% and 75%) TO:0000639 (Seed fertility) = Normal (Between 75% and 125%) For more information, please see this phenotype file
Mapping (Hover to Zoom-In)

Variant Information

Single base substitutions: 35

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	14890051	G-A	HET	INTERGENIC
SBS	Chr1	16423697	C-T	HET	INTERGENIC
SBS	Chr1	40924757	A-T	HET	INTERGENIC
SBS	Chr2	3534478	C-T	HOMO	INTERGENIC
SBS	Chr2	27728978	G-A	HET	UTR_3_PRIME
SBS	Chr3	5583695	A-G	HET	INTERGENIC
SBS	Chr3	11798386	C-G	HET	NON_SYNONYMOUS_CODING	LOC_Os03g20840
SBS	Chr4	8041936	T-G	HET	NON_SYNONYMOUS_CODING	LOC_Os04g14360
SBS	Chr4	10635666	C-G	HET	INTERGENIC
SBS	Chr4	13194631	G-A	HET	SYNONYMOUS_CODING
SBS	Chr4	15425357	C-T	HET	INTRON
SBS	Chr4	31271654	A-T	HET	INTERGENIC
SBS	Chr5	2565146	G-C	HET	NON_SYNONYMOUS_CODING	LOC_Os05g05240
SBS	Chr5	4919503	A-G	HET	NON_SYNONYMOUS_CODING	LOC_Os05g08890
SBS	Chr5	25907869	G-A	HET	INTERGENIC
SBS	Chr5	26770261	G-T	HET	INTERGENIC
SBS	Chr5	26770262	G-T	HET	INTERGENIC
SBS	Chr6	2452028	A-G	HET	INTERGENIC
SBS	Chr6	23771815	T-C	HET	INTERGENIC
SBS	Chr7	29652224	G-A	HET	INTERGENIC
SBS	Chr8	22336292	C-G	HOMO	INTERGENIC
SBS	Chr8	26207288	C-T	HET	INTERGENIC
SBS	Chr9	17393913	G-T	HOMO	UTR_5_PRIME
SBS	Chr9	17393914	A-T	HOMO	UTR_5_PRIME
SBS	Chr9	20963004	T-G	HET	INTRON
SBS	Chr10	12505601	A-G	HOMO	INTRON
SBS	Chr10	20727808	G-A	HET	NON_SYNONYMOUS_CODING	LOC_Os10g38900
SBS	Chr10	21290599	A-G	HOMO	INTERGENIC
SBS	Chr11	6004579	G-A	HET	INTERGENIC
SBS	Chr11	7056162	T-A	HET	INTERGENIC
SBS	Chr11	7056163	G-A	HET	INTERGENIC
SBS	Chr11	13619159	T-G	HET	INTERGENIC
SBS	Chr11	15481723	C-G	HET	INTERGENIC
SBS	Chr11	21142354	C-T	HET	INTERGENIC
SBS	Chr12	19422358	A-G	HET	INTERGENIC

Deletions: 22

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Deletion	Chr7	99862	99872	10
Deletion	Chr11	3565261	3565285	24	LOC_Os11g07150
Deletion	Chr4	4897041	4897046	5
Deletion	Chr6	4929215	4929226	11
Deletion	Chr4	7506716	7507038	322
Deletion	Chr3	8773228	8773237	9
Deletion	Chr4	8817747	8817749	2
Deletion	Chr5	9137829	9159308	21479	4
Deletion	Chr5	9687543	9687570	27
Deletion	Chr3	11992491	11992499	8
Deletion	Chr8	13425540	13425541	1
Deletion	Chr4	15167736	15167745	9
Deletion	Chr11	16278111	16278118	7
Deletion	Chr11	19132475	19132480	5
Deletion	Chr12	24167330	24167338	8
Deletion	Chr5	25633530	25633539	9
Deletion	Chr2	25856001	25945000	89000	13
Deletion	Chr2	26242668	26242697	29
Deletion	Chr11	27081231	27081235	4	LOC_Os11g44750
Deletion	Chr11	27995470	27995484	14
Deletion	Chr3	33165228	33165248	20
Deletion	Chr4	34890121	34890123	2

Insertions: 11

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Insertion	Chr2	15525799	15525799	1
Insertion	Chr1	40812809	40812810	2	LOC_Os01g70470
Insertion	Chr1	19824972	19824989	18	LOC_Os01g35789
Insertion	Chr1	1946332	1946333	2
Insertion	Chr1	24524866	24524869	4
Insertion	Chr3	25579459	25579460	2
Insertion	Chr5	2949653	2949653	1
Insertion	Chr5	24966616	24966616	1
Insertion	Chr6	4464678	4464681	4
Insertion	Chr10	17838567	17838570	4
Insertion	Chr12	2939720	2939720	1	LOC_Os12g06200

Inversions: 10

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr5	9137833	9156838
Inversion	Chr5	9156828	14817682	LOC_Os05g25480
Inversion	Chr5	9166471	9203596	LOC_Os05g16260
Inversion	Chr9	9437274	10237844
Inversion	Chr9	9437296	10237961
Inversion	Chr5	13929612	19404601	LOC_Os05g24150
Inversion	Chr5	14817308	19404597	LOC_Os05g25480
Inversion	Chr2	25855498	26095436
Inversion	Chr2	26324446	26454491	LOC_Os02g43620
Inversion	Chr2	26324675	26454506	LOC_Os02g43620

Translocations: 4

Variant Type	Chromosome	Position 1	Chromosome	Position 2	Number of Genes
Translocation	Chr4	4256199	Chr2	18648256
Translocation	Chr10	18557422	Chr4	7506722	2
Translocation	Chr10	18557423	Chr4	7506723	2
Translocation	Chr11	28290478	Chr4	12931276

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