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Mutant Information

Mutant Name	FN409-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN409-S Alignment File
Seed Availability	Yes [Order Seeds]
Phenotype	TO:0000430 (Germination Rate) = Low (Between 25% and 75%) For more information, please see this phenotype file
Mapping (Hover to Zoom-In)

Variant Information

Single base substitutions: 36

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	12215457	A-G	HET	INTERGENIC
SBS	Chr1	27873552	G-A	HOMO	INTERGENIC
SBS	Chr1	9782543	T-C	HOMO	INTERGENIC
SBS	Chr10	15936652	A-T	HET	UTR_3_PRIME
SBS	Chr11	17246426	A-G	HET	SYNONYMOUS_CODING
SBS	Chr11	2307978	G-T	HET	INTERGENIC
SBS	Chr11	2609676	C-T	HET	NON_SYNONYMOUS_CODING	LOC_Os11g05700
SBS	Chr12	1371226	C-T	HET	INTRON
SBS	Chr12	24067313	C-A	HET	NON_SYNONYMOUS_CODING	LOC_Os12g39120
SBS	Chr12	25214449	C-T	HET	INTERGENIC
SBS	Chr2	11502385	A-T	HET	INTERGENIC
SBS	Chr3	14182652	A-C	HET	INTERGENIC
SBS	Chr3	14272753	G-A	HET	INTERGENIC
SBS	Chr3	16997100	G-A	HET	NON_SYNONYMOUS_CODING	LOC_Os03g29810
SBS	Chr3	18817260	A-G	HOMO	INTERGENIC
SBS	Chr3	22061735	G-A	HET	INTERGENIC
SBS	Chr3	2628866	T-G	HET	INTRON
SBS	Chr3	35444403	T-C	HET	INTERGENIC
SBS	Chr4	21215831	G-A	HOMO	UTR_3_PRIME
SBS	Chr4	24281550	C-A	HET	NON_SYNONYMOUS_CODING	LOC_Os04g40910
SBS	Chr5	13252411	C-T	HET	SYNONYMOUS_CODING
SBS	Chr5	19926657	C-G	HET	INTRON
SBS	Chr5	2009262	T-A	HOMO	INTERGENIC
SBS	Chr5	21926901	T-C	HET	UTR_3_PRIME
SBS	Chr5	27379408	T-C	HET	INTRON
SBS	Chr5	416525	T-A	HOMO	INTRON
SBS	Chr5	6762351	T-G	HOMO	INTERGENIC
SBS	Chr5	9662277	C-T	HET	INTRON
SBS	Chr6	20692121	G-C	HET	INTERGENIC
SBS	Chr7	1049830	C-T	HET	INTERGENIC
SBS	Chr7	6783730	T-C	HOMO	INTERGENIC
SBS	Chr8	11592499	C-A	HET	INTERGENIC
SBS	Chr8	13816574	G-A	HET	SYNONYMOUS_CODING
SBS	Chr8	532431	C-A	HOMO	INTERGENIC
SBS	Chr9	20584643	C-G	HOMO	INTERGENIC
SBS	Chr9	2110542	G-C	HET	NON_SYNONYMOUS_CODING	LOC_Os09g04080

Deletions: 19

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Deletion	Chr5	68590	68592	2	LOC_Os05g01040
Deletion	Chr11	1283926	1283941	15
Deletion	Chr12	1991929	1991934	5
Deletion	Chr12	3883649	3883653	4
Deletion	Chr7	4095483	4095517	34
Deletion	Chr6	4232409	4232414	5
Deletion	Chr3	4801149	4801163	14
Deletion	Chr4	6511832	6511850	18	LOC_Os04g11880
Deletion	Chr7	8170589	8170594	5
Deletion	Chr10	13704106	13704118	12
Deletion	Chr8	13769429	13769442	13
Deletion	Chr10	13837088	13837098	10
Deletion	Chr3	14102795	14102797	2
Deletion	Chr6	14162062	14162067	5
Deletion	Chr2	14296594	14296599	5
Deletion	Chr12	16854269	16854270	1
Deletion	Chr1	21612333	21612344	11
Deletion	Chr12	24112379	24112380	1
Deletion	Chr4	28205958	28214147	8189	2

Insertions: 3

Variant Type	Chromosome	Start	End	Size (bp)
Insertion	Chr1	26040912	26040912	1
Insertion	Chr2	22251574	22251574	1
Insertion	Chr3	7620255	7620256	2

Inversions: 1

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr4	6282940	7223082

Translocations: 2

Variant Type	Chromosome	Position 1	Chromosome	Position 2	Number of Genes
Translocation	Chr6	23463353	Chr3	29226757	LOC_Os06g39515
Translocation	Chr11	25330902	Chr7	6596893

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