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Mutant Information

Mutant Name	FN2976-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN2976-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: 57

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	25119541	G-A	HET	INTERGENIC
SBS	Chr1	25601181	T-A	HOMO	INTERGENIC
SBS	Chr1	29501608	G-T	HET	INTRON
SBS	Chr1	30547773	A-T	HET	INTERGENIC
SBS	Chr1	39162934	G-A	HET	INTRON
SBS	Chr1	40234506	T-A	HET	INTERGENIC
SBS	Chr2	5434862	C-T	HET	NON_SYNONYMOUS_CODING	LOC_Os02g10340
SBS	Chr2	11342559	T-C	HET	INTRON
SBS	Chr2	11617149	C-T	HET	SYNONYMOUS_CODING
SBS	Chr2	14074470	C-T	HET	STOP_GAINED	LOC_Os02g24270
SBS	Chr2	15369919	C-T	HET	INTRON
SBS	Chr2	25054956	C-T	HET	SYNONYMOUS_CODING
SBS	Chr2	25544498	A-T	HET	INTRON
SBS	Chr2	26900677	C-T	HET	SYNONYMOUS_CODING
SBS	Chr2	29564291	A-G	HET	INTERGENIC
SBS	Chr2	31963575	G-A	HET	INTERGENIC
SBS	Chr2	35073305	C-A	HET	INTERGENIC
SBS	Chr3	14769442	T-C	HET	INTERGENIC
SBS	Chr3	33512119	T-C	HOMO	INTERGENIC
SBS	Chr4	1671003	G-A	HET	INTERGENIC
SBS	Chr4	25641322	G-T	HET	INTRON
SBS	Chr5	271877	T-A	HET	STOP_GAINED	LOC_Os05g01470
SBS	Chr5	3367296	C-T	HET	INTERGENIC
SBS	Chr5	9381874	A-G	HET	INTERGENIC
SBS	Chr5	16972535	C-G	HOMO	INTERGENIC
SBS	Chr6	24864633	C-A	HOMO	INTERGENIC
SBS	Chr6	25423317	G-A	HET	INTERGENIC
SBS	Chr6	27084456	T-C	HET	INTERGENIC
SBS	Chr6	29630642	G-A	HET	NON_SYNONYMOUS_CODING	LOC_Os06g48940
SBS	Chr7	305429	G-A	HET	INTERGENIC
SBS	Chr7	9186663	G-C	HET	INTERGENIC
SBS	Chr7	16643195	A-C	HET	INTERGENIC
SBS	Chr8	12101224	G-A	HET	INTERGENIC
SBS	Chr8	15465978	A-G	HET	INTERGENIC
SBS	Chr8	16455893	C-T	HET	INTERGENIC
SBS	Chr8	18748615	G-A	HET	INTERGENIC
SBS	Chr8	26023826	T-C	HET	INTERGENIC
SBS	Chr8	27061008	C-T	HET	INTERGENIC
SBS	Chr8	28038340	G-A	HET	INTERGENIC
SBS	Chr9	9271631	G-A	HET	INTERGENIC
SBS	Chr9	11069339	T-G	HET	INTERGENIC
SBS	Chr9	16935263	A-T	HET	INTRON
SBS	Chr10	3667063	C-T	HET	INTERGENIC
SBS	Chr10	4110545	C-T	HET	INTERGENIC
SBS	Chr10	8413658	G-A	HET	NON_SYNONYMOUS_CODING	LOC_Os10g16880
SBS	Chr10	8933068	T-G	HET	INTERGENIC
SBS	Chr10	21685716	G-A	HET	INTERGENIC
SBS	Chr11	5693388	G-C	HET	INTERGENIC
SBS	Chr11	8340887	A-G	HET	INTERGENIC
SBS	Chr11	11533296	C-T	HET	INTERGENIC
SBS	Chr11	14907398	C-T	HET	INTERGENIC
SBS	Chr11	20441738	G-C	HOMO	INTERGENIC
SBS	Chr12	7520493	G-A	HOMO	INTERGENIC
SBS	Chr12	19755833	T-C	HET	NON_SYNONYMOUS_CODING	LOC_Os12g32710
SBS	Chr12	22794594	C-T	HET	INTERGENIC
SBS	Chr12	23556428	C-T	HET	NON_SYNONYMOUS_CODING	LOC_Os12g38400
SBS	Chr12	25306611	C-T	HET	INTRON

Deletions: 32

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Deletion	Chr5	3852005	3852007	2
Deletion	Chr8	5935232	5935233	1
Deletion	Chr8	6324712	6324723	11
Deletion	Chr4	8018093	8018095	2	LOC_Os04g14304
Deletion	Chr3	8081706	8081734	28
Deletion	Chr10	9318287	9318289	2
Deletion	Chr3	11475167	11475168	1
Deletion	Chr10	12476285	12476290	5	LOC_Os10g24350
Deletion	Chr8	13398109	13398111	2
Deletion	Chr10	16180635	16180648	13
Deletion	Chr2	16434103	16434104	1	LOC_Os02g27750
Deletion	Chr7	16665498	16665501	3	LOC_Os07g28470
Deletion	Chr3	18125984	18125988	4
Deletion	Chr12	19312845	19312849	4
Deletion	Chr2	19514001	19605000	90999	12
Deletion	Chr2	19610001	19680000	69999	12
Deletion	Chr2	19682001	19903000	220999	35
Deletion	Chr2	19912001	20205000	292999	40
Deletion	Chr2	20213001	20289000	75999	8
Deletion	Chr2	20294001	20505000	210999	23
Deletion	Chr2	22420096	22420098	2
Deletion	Chr7	24005581	24005582	1
Deletion	Chr1	24824001	25033000	208999	29
Deletion	Chr1	25036001	25102000	65999	10
Deletion	Chr1	25203001	25690000	486999	69
Deletion	Chr4	25287148	25287149	1
Deletion	Chr12	26523896	26523904	8
Deletion	Chr6	27349317	27349318	1
Deletion	Chr2	32086053	32086055	2
Deletion	Chr1	33786001	33846000	59999	12
Deletion	Chr1	34073213	34073215	2
Deletion	Chr1	34316982	34316994	12

Insertions: 8

Variant Type	Chromosome	Start	End	Size (bp)
Insertion	Chr2	10468250	10468250	1
Insertion	Chr2	19518604	19518604	1
Insertion	Chr4	1453867	1453872	6
Insertion	Chr6	18041867	18041867	1
Insertion	Chr10	7000089	7000173	85
Insertion	Chr12	12054206	12054206	1
Insertion	Chr12	18255869	18255869	1
Insertion	Chr12	19099706	19099706	1

Inversions: 5

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr9	16920196	16933278	LOC_Os09g27810
Inversion	Chr9	16920221	16934633	2
Inversion	Chr1	24825310	25125728
Inversion	Chr4	28688777	28688915
Inversion	Chr1	33781930	33926453

Translocations: 4

Variant Type	Chromosome	Position 1	Chromosome	Position 2	Number of Genes
Translocation	Chr9	16933291	Chr1	33926482
Translocation	Chr9	16934620	Chr1	33878053	LOC_Os09g27830
Translocation	Chr4	19146627	Chr3	17621955
Translocation	Chr4	30287006	Chr3	744330	LOC_Os03g02230

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