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Mutant Information

Mutant Name	FN1561-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN1561-S Alignment File
Seed Availability	Yes [Order Seeds]
Phenotype	TO:0000326 (Leaf Color) = Normal TO:0000346 (Tiller number) = 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: 60

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	10546350	C-T	HET	NON_SYNONYMOUS_CODING	LOC_Os01g18700
SBS	Chr1	13723501	G-T	HET	INTERGENIC
SBS	Chr1	15232696	A-T	HET	INTERGENIC
SBS	Chr1	15664982	G-A	HET	INTERGENIC
SBS	Chr1	19685526	A-T	HET	INTRON
SBS	Chr1	24292437	C-T	Homo	INTERGENIC
SBS	Chr1	39667120	G-A	HET	INTRON
SBS	Chr10	11061856	A-C	HET	INTERGENIC
SBS	Chr10	15038340	A-T	HET	INTERGENIC
SBS	Chr10	9351973	G-A	HET	INTRON
SBS	Chr11	10844075	C-A	HET	INTERGENIC
SBS	Chr11	13256182	G-A	HET	INTRON
SBS	Chr11	13928659	G-A	HET	INTERGENIC
SBS	Chr11	15175691	C-A	HET	NON_SYNONYMOUS_CODING	LOC_Os11g26480
SBS	Chr11	16798793	A-G	HET	INTERGENIC
SBS	Chr11	20177120	C-G	HET	INTERGENIC
SBS	Chr11	25434957	G-A	HET	INTERGENIC
SBS	Chr11	9047887	C-A	HET	INTERGENIC
SBS	Chr12	18801542	A-T	HET	INTERGENIC
SBS	Chr12	18801543	G-T	HET	INTERGENIC
SBS	Chr12	26357669	A-T	Homo	INTERGENIC
SBS	Chr12	5665446	T-G	HET	INTERGENIC
SBS	Chr12	6919730	G-A	HET	INTERGENIC
SBS	Chr12	8032818	T-C	HET	INTRON
SBS	Chr2	2791140	C-T	Homo	INTERGENIC
SBS	Chr2	29921110	T-A	HET	INTERGENIC
SBS	Chr2	3598467	C-T	Homo	INTERGENIC
SBS	Chr3	19366749	A-G	HET	INTRON
SBS	Chr3	20832214	C-T	Homo	INTRON
SBS	Chr3	23248550	C-T	Homo	INTERGENIC
SBS	Chr3	30157618	C-T	Homo	INTRON
SBS	Chr3	4512859	G-A	HET	INTERGENIC
SBS	Chr3	7129959	C-T	Homo	INTRON
SBS	Chr4	10630720	C-A	HET	INTERGENIC
SBS	Chr4	11145129	G-A	HET	NON_SYNONYMOUS_CODING	LOC_Os04g19990
SBS	Chr4	16965101	A-G	HET	INTERGENIC
SBS	Chr4	20270409	G-A	HET	INTERGENIC
SBS	Chr4	2902454	C-T	HET	INTRON
SBS	Chr5	12804950	G-A	HET	INTERGENIC
SBS	Chr5	14170159	G-T	HET	INTERGENIC
SBS	Chr5	17516657	G-A	HET	NON_SYNONYMOUS_CODING	LOC_Os05g30220
SBS	Chr5	27210441	T-G	HET	INTERGENIC
SBS	Chr5	27923625	G-A	Homo	NON_SYNONYMOUS_CODING	LOC_Os05g48710
SBS	Chr5	5556666	A-G	HET	INTERGENIC
SBS	Chr6	17973048	G-T	HET	INTERGENIC
SBS	Chr6	24284966	C-T	HET	INTERGENIC
SBS	Chr6	4767770	T-A	HET	INTERGENIC
SBS	Chr7	12403177	C-T	Homo	INTERGENIC
SBS	Chr8	13813346	G-A	HET	INTERGENIC
SBS	Chr8	24826593	A-T	Homo	INTERGENIC
SBS	Chr8	25703346	A-T	HET	INTRON
SBS	Chr8	27540871	G-A	HET	INTERGENIC
SBS	Chr8	9670621	G-A	HET	NON_SYNONYMOUS_CODING	LOC_Os08g15880
SBS	Chr9	10077839	C-A	HET	INTRON
SBS	Chr9	19674789	G-T	HET	SYNONYMOUS_CODING
SBS	Chr9	19674790	G-T	HET	NON_SYNONYMOUS_CODING	LOC_Os09g32964
SBS	Chr9	22410881	G-A	HET	INTRON
SBS	Chr9	3997712	C-T	Homo	NON_SYNONYMOUS_CODING	LOC_Os09g07860
SBS	Chr9	5235311	T-C	HET	INTRON
SBS	Chr9	697206	C-T	HET	INTRON

Deletions: 47

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Deletion	Chr7	170870	170873	3
Deletion	Chr10	609301	609302	1
Deletion	Chr7	3855484	3855486	2
Deletion	Chr4	5066942	5066943	1
Deletion	Chr2	6638812	6638820	8	LOC_Os02g12690
Deletion	Chr10	7770267	7770268	1
Deletion	Chr9	8023478	8023481	3	LOC_Os09g13710
Deletion	Chr1	8219688	8219690	2
Deletion	Chr9	8610790	8610791	1
Deletion	Chr4	8774490	8774494	4
Deletion	Chr9	9055287	9055288	1	LOC_Os09g15020
Deletion	Chr7	9728966	9728969	3
Deletion	Chr8	9912385	9912387	2
Deletion	Chr1	10242633	10242634	1
Deletion	Chr9	10816466	10816467	1
Deletion	Chr4	11128621	11128622	1
Deletion	Chr6	11183396	11183418	22
Deletion	Chr8	11336106	11336107	1	LOC_Os08g18990
Deletion	Chr7	11354958	11354960	2
Deletion	Chr6	13029627	13029628	1
Deletion	Chr6	13086576	13086584	8	LOC_Os06g22520
Deletion	Chr8	13898483	13898484	1
Deletion	Chr8	14441033	14441034	1
Deletion	Chr11	14806545	14806553	8
Deletion	Chr1	16290790	16290791	1
Deletion	Chr2	16436186	16436187	1	LOC_Os02g27750
Deletion	Chr4	16812853	16812854	1
Deletion	Chr4	17016600	17016612	12
Deletion	Chr2	18802620	18802621	1
Deletion	Chr12	18897960	18897963	3
Deletion	Chr7	19245128	19245131	3
Deletion	Chr9	19575681	19581250	5569	LOC_Os09g32830
Deletion	Chr12	19761757	19761768	11
Deletion	Chr6	20382925	20382928	3
Deletion	Chr6	20496905	20496906	1
Deletion	Chr7	22370967	22370974	7	LOC_Os07g37350
Deletion	Chr4	23435488	23435495	7
Deletion	Chr3	24070052	24070059	7
Deletion	Chr6	24604853	24604854	1
Deletion	Chr6	24658443	24658464	21
Deletion	Chr4	26335759	26335763	4
Deletion	Chr5	27791966	27791967	1
Deletion	Chr6	29095453	29107115	11662	2
Deletion	Chr2	31215776	31215777	1
Deletion	Chr3	31637977	31637983	6
Deletion	Chr1	39533490	39533514	24
Deletion	Chr1	40516455	40516456	1

Insertions: 12

Variant Type	Chromosome	Start	End	Size (bp)
Insertion	Chr1	14681959	14681962	4
Insertion	Chr1	30087385	30087385	1
Insertion	Chr11	22562917	22562918	2
Insertion	Chr12	12091021	12091032	12
Insertion	Chr12	4435501	4435502	2
Insertion	Chr3	8491716	8491716	1
Insertion	Chr4	7471318	7471318	1
Insertion	Chr5	14520416	14520417	2
Insertion	Chr6	2906012	2906017	6
Insertion	Chr6	5855839	5855844	6
Insertion	Chr8	16840942	16840942	1
Insertion	Chr8	9230878	9230903	26

Inversions: 5

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr11	8457811	8476601	LOC_Os11g15030
Inversion	Chr11	8476603	8513902	LOC_Os11g15120
Inversion	Chr8	15166096	15237330	LOC_Os08g25010
Inversion	Chr8	15237319	15320761
Inversion	Chr1	40371445	40748258	LOC_Os01g70340

Translocations: 3

Variant Type	Chromosome	Position 1	Chromosome	Position 2	Number of Genes
Translocation	Chr11	8457815	Chr4	34434699	LOC_Os11g15030
Translocation	Chr11	8458705	Chr4	34435452	LOC_Os11g15030
Translocation	Chr6	15747380	Chr4	19596842

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