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Mutant Information

Mutant Name	FN2973-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN2973-S Alignment File
Seed Availability	Yes [Order Seeds]
Phenotype	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: 56

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	13540139	C-G	HET	INTRON
SBS	Chr1	32994875	T-C	HOMO	INTERGENIC
SBS	Chr1	37800867	C-T	HOMO	INTERGENIC
SBS	Chr1	7966821	C-A	HET	INTERGENIC
SBS	Chr10	11987795	G-T	HET	INTERGENIC
SBS	Chr11	26132492	C-G	HET	INTERGENIC
SBS	Chr11	26409166	A-G	HET	INTERGENIC
SBS	Chr11	4298088	C-T	HET	INTERGENIC
SBS	Chr11	4791088	C-T	HET	INTERGENIC
SBS	Chr11	4831135	C-A	HET	INTRON
SBS	Chr11	7569712	G-A	HET	INTERGENIC
SBS	Chr11	833876	C-T	HOMO	INTERGENIC
SBS	Chr12	16109750	C-T	HET	NON_SYNONYMOUS_CODING	LOC_Os12g27390
SBS	Chr12	18235845	T-A	HET	INTERGENIC
SBS	Chr12	22267817	G-A	HET	INTERGENIC
SBS	Chr12	5187505	G-A	HET	INTERGENIC
SBS	Chr12	8714962	G-A	HET	INTERGENIC
SBS	Chr2	10742427	T-C	HET	INTRON
SBS	Chr2	11233365	C-G	HET	INTERGENIC
SBS	Chr2	31617688	T-C	HET	INTERGENIC
SBS	Chr2	6364206	A-T	HET	INTERGENIC
SBS	Chr3	14290451	A-T	HET	INTRON
SBS	Chr3	18459228	T-C	HET	INTERGENIC
SBS	Chr3	26343610	G-A	HET	NON_SYNONYMOUS_CODING	LOC_Os03g46560
SBS	Chr4	18089523	A-G	HET	INTRON
SBS	Chr5	10892345	G-A	HET	INTERGENIC
SBS	Chr5	11974130	A-C	HOMO	NON_SYNONYMOUS_CODING	LOC_Os05g20410
SBS	Chr5	20408033	T-A	HET	INTERGENIC
SBS	Chr5	20408034	G-A	HET	INTERGENIC
SBS	Chr5	26274806	G-C	HET	INTERGENIC
SBS	Chr5	26904466	C-T	HOMO	INTRON
SBS	Chr6	13800258	G-A	HET	INTERGENIC
SBS	Chr6	19653491	T-C	HET	INTERGENIC
SBS	Chr6	23327787	C-T	HET	NON_SYNONYMOUS_CODING	LOC_Os06g39310
SBS	Chr6	24956253	G-A	HET	UTR_3_PRIME
SBS	Chr6	26572790	C-T	HET	INTERGENIC
SBS	Chr6	4344479	A-T	HET	INTERGENIC
SBS	Chr6	5062857	G-A	HOMO	INTRON
SBS	Chr6	7914609	C-T	HET	INTERGENIC
SBS	Chr6	8231653	G-T	HET	SYNONYMOUS_CODING
SBS	Chr6	9539182	G-T	HET	INTERGENIC
SBS	Chr7	11526318	C-T	HET	INTERGENIC
SBS	Chr7	12698808	A-G	HET	INTERGENIC
SBS	Chr7	13278418	G-C	HET	NON_SYNONYMOUS_CODING	LOC_Os07g23494
SBS	Chr7	1472759	C-G	HET	INTERGENIC
SBS	Chr7	24655402	C-A	HET	NON_SYNONYMOUS_CODING	LOC_Os07g41180
SBS	Chr7	26573216	G-A	HET	INTRON
SBS	Chr7	29600924	G-A	HET	SPLICE_SITE_REGION
SBS	Chr7	3137	T-C	HET	INTERGENIC
SBS	Chr8	10199585	C-A	HET	INTRON
SBS	Chr8	11146268	C-T	HET	INTRON
SBS	Chr8	24132803	G-T	HET	INTRON
SBS	Chr8	2607372	G-A	HET	INTRON
SBS	Chr8	3881243	T-C	HET	INTERGENIC
SBS	Chr8	4000676	C-T	HOMO	STOP_GAINED	LOC_Os08g07140
SBS	Chr9	11608927	G-A	HET	INTRON

Deletions: 30

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Deletion	Chr6	3814976	3814977	1	LOC_Os06g07850
Deletion	Chr8	4340609	4340611	2
Deletion	Chr4	5185465	5185468	3
Deletion	Chr6	6073829	6073832	3
Deletion	Chr11	11664802	11664803	1
Deletion	Chr6	12403195	12403196	1
Deletion	Chr12	13193504	13193505	1
Deletion	Chr8	13807996	13807997	1
Deletion	Chr4	14858156	14858157	1	LOC_Os04g25640
Deletion	Chr12	16145252	16145258	6	LOC_Os12g27440
Deletion	Chr1	17379662	17379667	5
Deletion	Chr5	17389650	17389668	18
Deletion	Chr9	17902643	17902659	16
Deletion	Chr7	18048001	18148000	99999	14
Deletion	Chr7	18097958	18097973	15	LOC_Os07g30580
Deletion	Chr7	18591314	18591326	12
Deletion	Chr5	20385735	20385745	10
Deletion	Chr9	20388264	20388279	15
Deletion	Chr2	20404001	20513000	108999	15
Deletion	Chr2	20530001	20637000	106999	12
Deletion	Chr2	20644001	20854000	209999	32
Deletion	Chr6	22233654	22233668	14
Deletion	Chr7	22712958	22712968	10
Deletion	Chr11	23968463	23968464	1
Deletion	Chr7	27330236	27330252	16
Deletion	Chr7	27652520	27652526	6
Deletion	Chr6	28305911	28305913	2
Deletion	Chr6	28742544	28742558	14
Deletion	Chr1	32624724	32624731	7
Deletion	Chr3	34754109	34754111	2	LOC_Os03g61190

Insertions: 11

Variant Type	Chromosome	Start	End	Size (bp)
Insertion	Chr10	11844757	11844757	1
Insertion	Chr11	18372518	18372583	66
Insertion	Chr12	23764589	23764681	93
Insertion	Chr2	13376773	13376808	36
Insertion	Chr2	6797130	6797132	3
Insertion	Chr4	28760012	28760013	2
Insertion	Chr5	22511899	22511909	11
Insertion	Chr5	29017191	29017192	2
Insertion	Chr7	2495911	2495945	35
Insertion	Chr8	25824153	25824154	2
Insertion	Chr8	28412508	28412595	88

Inversions: 9

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr5	2644354	2644957
Inversion	Chr2	12670583	12670911
Inversion	Chr1	12927356	12927470
Inversion	Chr3	21619183	21620636	LOC_Os03g38920
Inversion	Chr4	22650339	22651489	LOC_Os04g38060
Inversion	Chr2	31288552	32097842
Inversion	Chr2	31288556	32097844
Inversion	Chr1	37731485	37903887
Inversion	Chr1	37731490	37903887

Translocations: 7

Variant Type	Chromosome	Position 1	Chromosome	Position 2	Number of Genes
Translocation	Chr8	12359800	Chr5	20684292
Translocation	Chr11	15452229	Chr2	15839407
Translocation	Chr11	15452548	Chr2	15839405
Translocation	Chr12	17125596	Chr4	27671344
Translocation	Chr12	17125831	Chr4	27671334
Translocation	Chr7	18143618	Chr4	131931	LOC_Os07g30660
Translocation	Chr12	26145426	Chr11	17687332

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