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Mutant Information

Mutant Name	FN2142-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN2142-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	12033484	G-C	HET
SBS	Chr1	20955243	C-A	HET	NON_SYNONYMOUS_CODING	LOC_Os01g37510
SBS	Chr1	24094948	T-C	HET
SBS	Chr1	32712933	T-A	HET
SBS	Chr2	19517941	C-T	HET
SBS	Chr2	21339428	G-A	HET
SBS	Chr2	30787516	T-C	HET
SBS	Chr3	10505702	C-T	Homo
SBS	Chr3	16828236	A-G	HET	NON_SYNONYMOUS_CODING	LOC_Os03g29520
SBS	Chr3	17852713	G-T	HET
SBS	Chr4	1318296	C-A	HET
SBS	Chr4	3211659	T-C	HET
SBS	Chr4	7730717	T-C	HET	NON_SYNONYMOUS_CODING	LOC_Os04g13860
SBS	Chr4	20833084	C-A	Homo
SBS	Chr4	21778745	A-G	HET
SBS	Chr6	6561574	C-G	HET	NON_SYNONYMOUS_CODING	LOC_Os06g12220
SBS	Chr6	27607057	A-C	Homo
SBS	Chr7	20219591	G-A	HET
SBS	Chr7	20977021	T-A	HET
SBS	Chr7	27999675	T-C	Homo
SBS	Chr8	19033267	G-A	Homo
SBS	Chr8	19033269	G-T	Homo
SBS	Chr8	19033270	G-T	Homo
SBS	Chr9	4173903	C-T	HET
SBS	Chr9	10900226	T-C	HET
SBS	Chr9	13945952	A-G	HET
SBS	Chr9	15815397	A-T	HET
SBS	Chr10	3329834	A-C	Homo
SBS	Chr10	3329838	T-A	Homo
SBS	Chr10	11268834	C-T	HET
SBS	Chr10	12252928	T-G	HET
SBS	Chr10	22905633	G-T	Homo
SBS	Chr11	15323452	T-A	HET
SBS	Chr11	17624002	C-G	HET
SBS	Chr11	24629914	G-T	HET	NON_SYNONYMOUS_CODING	LOC_Os11g41110
SBS	Chr12	3751589	C-T	Homo

Deletions: 13

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Deletion	Chr9	702402	702420	18
Deletion	Chr9	5374723	5374724	1	LOC_Os09g09880
Deletion	Chr8	6616637	6616642	5
Deletion	Chr7	9359689	9359690	1	LOC_Os07g16054
Deletion	Chr9	11104043	11104044	1
Deletion	Chr1	14842177	14842181	4
Deletion	Chr12	20240099	20240100	1
Deletion	Chr4	20756980	20756981	1
Deletion	Chr8	20764814	20764816	2
Deletion	Chr4	21755011	21755025	14
Deletion	Chr12	22319737	22319818	81
Deletion	Chr6	25547398	25547400	2
Deletion	Chr6	27170394	27170396	2

Insertions: 7

Variant Type	Chromosome	Start	End	Size (bp)
Insertion	Chr9	1973138	1973138	1
Insertion	Chr6	20321735	20321736	2
Insertion	Chr8	16832934	16832935	2
Insertion	Chr10	3806106	3806113	8
Insertion	Chr11	6663033	6663036	4
Insertion	Chr11	22388538	22388549	12
Insertion	Chr12	21760065	21760066	2

Inversions: 44

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr1	424637	425054	LOC_Os01g01800
Inversion	Chr5	1011121	1011470	LOC_Os05g02810
Inversion	Chr10	1078041	1078506	LOC_Os10g02740
Inversion	Chr5	1110863	1111248
Inversion	Chr6	1427027	1427322	LOC_Os06g03660
Inversion	Chr12	2990343	2990650	LOC_Os12g06270
Inversion	Chr6	4466493	4466799
Inversion	Chr4	5846620	5846936	LOC_Os04g10750
Inversion	Chr2	6478412	6478598	LOC_Os02g12420
Inversion	Chr6	6549137	6549346
Inversion	Chr1	6842197	6842551	LOC_Os01g12480
Inversion	Chr6	7844234	7844545	LOC_Os06g14060
Inversion	Chr11	8020254	8020387	LOC_Os11g14300
Inversion	Chr10	8759806	8759913	LOC_Os10g17380
Inversion	Chr11	8791394	8791529	LOC_Os11g15520
Inversion	Chr1	9593435	9593797
Inversion	Chr2	9976764	9977305	LOC_Os02g17350
Inversion	Chr2	10158877	10159084	LOC_Os02g17650
Inversion	Chr1	11090023	11090311	LOC_Os01g19548
Inversion	Chr8	11448263	11448454	LOC_Os08g19140
Inversion	Chr7	11618009	11618193
Inversion	Chr11	11809048	11809537	LOC_Os11g20400
Inversion	Chr6	12277015	12277485
Inversion	Chr12	12784092	12784208	LOC_Os12g22620
Inversion	Chr10	14176631	14177199
Inversion	Chr12	14239240	14239532
Inversion	Chr5	14654022	14654236
Inversion	Chr7	16779292	16779591
Inversion	Chr11	16791085	16791428
Inversion	Chr4	17888432	18052674	LOC_Os04g29990
Inversion	Chr5	18585244	18585538
Inversion	Chr10	19171257	19171674
Inversion	Chr9	19260416	19260662	LOC_Os09g32270
Inversion	Chr11	19480513	19480749
Inversion	Chr11	20522336	20523101	LOC_Os11g35030
Inversion	Chr5	24188161	24188562	LOC_Os05g41290
Inversion	Chr11	24900109	24900308	LOC_Os11g41520
Inversion	Chr4	25111554	25112042	LOC_Os04g42430
Inversion	Chr5	27759996	27760401	LOC_Os05g48416
Inversion	Chr5	29523205	29523436	LOC_Os05g51490
Inversion	Chr4	30274576	30274767	LOC_Os04g51120
Inversion	Chr3	30396911	30397012	LOC_Os03g53000
Inversion	Chr1	41166427	41166741	LOC_Os01g71130
Inversion	Chr1	41862550	41862689	LOC_Os01g72190

Translocations: 16

Variant Type	Chromosome	Position 1	Chromosome	Position 2	Number of Genes
Translocation	Chr10	467829	Chr1	30237136
Translocation	Chr9	1382629	Chr8	9939475	2
Translocation	Chr3	2467051	Chr2	27134605	2
Translocation	Chr3	2467063	Chr2	27133945	LOC_Os03g05060
Translocation	Chr11	5107201	Chr8	3855213	LOC_Os11g09530
Translocation	Chr10	7362075	Chr6	10381237
Translocation	Chr7	11077853	Chr4	29420442	2
Translocation	Chr11	12720352	Chr3	6152897	2
Translocation	Chr11	12720695	Chr3	6149996	LOC_Os11g22160
Translocation	Chr8	15015619	Chr6	14816504	LOC_Os08g24810
Translocation	Chr10	15471883	Chr7	22106137
Translocation	Chr10	15472085	Chr7	22106131
Translocation	Chr8	16385243	Chr7	15520214
Translocation	Chr12	18616684	Chr5	6798102
Translocation	Chr11	19735588	Chr5	2392225
Translocation	Chr12	22023465	Chr8	27373387

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