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Mutant Information

Mutant Name	FN1606-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN1606-S Alignment File
Seed Availability	Yes [Order Seeds]
Phenotype	TO:0000014 (Panicle Weight) = Low (Between 25% and 74%) TO:0000207 (Plant height) = Normal (Between 75% and 125%) TO:0000445 (Seed Number) = Low (Between 25% and 74%) TO:0000639 (Seed fertility) = Normal (Between 75% and 125%) 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	24912376	C-T	HET	INTERGENIC
SBS	Chr1	32570228	A-G	Homo	INTERGENIC
SBS	Chr10	12101135	G-A	Homo	INTERGENIC
SBS	Chr10	13811219	C-G	HET	INTERGENIC
SBS	Chr10	1521065	G-T	HET	INTERGENIC
SBS	Chr10	1521066	A-T	HET	INTERGENIC
SBS	Chr10	20098944	C-A	HET	NON_SYNONYMOUS_CODING	LOC_Os10g37540
SBS	Chr10	8600367	G-C	Homo	INTERGENIC
SBS	Chr11	10111159	A-T	HET	NON_SYNONYMOUS_CODING	LOC_Os11g17990
SBS	Chr11	14601258	T-G	HET	INTERGENIC
SBS	Chr11	15118666	G-T	HET	INTERGENIC
SBS	Chr11	18840209	A-C	HET	INTERGENIC
SBS	Chr11	22839130	C-T	HET	INTERGENIC
SBS	Chr12	8153564	G-T	HET	INTERGENIC
SBS	Chr2	23347680	G-A	HET	INTRON
SBS	Chr2	27604955	G-A	HET	SYNONYMOUS_CODING
SBS	Chr2	30499378	G-A	HET	INTERGENIC
SBS	Chr3	11531601	G-A	Homo	INTRON
SBS	Chr3	3062859	G-A	HET	STOP_GAINED	LOC_Os03g06110
SBS	Chr4	17156330	C-G	Homo	NON_SYNONYMOUS_CODING	LOC_Os04g28940
SBS	Chr4	24421969	T-C	Homo	INTERGENIC
SBS	Chr4	2472892	A-T	Homo	INTERGENIC
SBS	Chr4	32960967	A-T	HET	INTERGENIC
SBS	Chr4	32960968	C-A	HET	INTERGENIC
SBS	Chr5	12323574	A-G	Homo	INTERGENIC
SBS	Chr5	17932767	C-T	HET	NON_SYNONYMOUS_CODING	LOC_Os05g30880
SBS	Chr5	8576398	G-A	Homo	INTRON
SBS	Chr6	17552267	G-T	Homo	INTRON
SBS	Chr6	27865070	C-G	HET	INTERGENIC
SBS	Chr6	27865071	C-T	HET	INTERGENIC
SBS	Chr6	31199284	G-A	HET	INTERGENIC
SBS	Chr7	14381654	G-A	HET	INTERGENIC
SBS	Chr7	29004699	C-T	HET	INTRON
SBS	Chr7	6730941	A-G	HET	INTERGENIC
SBS	Chr8	10236866	A-G	Homo	INTERGENIC
SBS	Chr9	1605135	G-T	Homo	INTERGENIC

Deletions: 40

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Deletion	Chr8	524553	524566	13
Deletion	Chr8	2346895	2346898	3
Deletion	Chr8	2607364	2607365	1
Deletion	Chr3	2672178	2672202	24
Deletion	Chr9	2981590	2981591	1
Deletion	Chr1	6712671	6712675	4	LOC_Os01g12290
Deletion	Chr8	6819863	6819873	10	LOC_Os08g11620
Deletion	Chr6	7546035	7546036	1	LOC_Os06g13630
Deletion	Chr3	7619219	7619220	1
Deletion	Chr12	8281938	8281942	4
Deletion	Chr12	8893563	8893564	1
Deletion	Chr10	9298834	9298835	1	LOC_Os10g18294
Deletion	Chr7	9610637	9610650	13
Deletion	Chr1	9898681	9898683	2
Deletion	Chr2	10562542	10562556	14
Deletion	Chr9	11331683	11331689	6
Deletion	Chr11	15531553	15531556	3	LOC_Os11g26990
Deletion	Chr2	15725977	15725978	1
Deletion	Chr12	15792948	15792964	16
Deletion	Chr8	17818069	17818070	1
Deletion	Chr11	18050966	18050967	1
Deletion	Chr8	18553674	18563755	10081	3
Deletion	Chr11	18679639	18679696	57
Deletion	Chr9	19548665	19548673	8
Deletion	Chr1	21829282	21829283	1
Deletion	Chr2	22179031	22179048	17
Deletion	Chr2	22532370	22532371	1
Deletion	Chr10	23135804	23135806	2
Deletion	Chr2	23533779	23533782	3
Deletion	Chr1	25965401	25965404	3
Deletion	Chr1	25991001	26077000	86000	14
Deletion	Chr11	26803624	26803647	23
Deletion	Chr7	27513761	27513764	3
Deletion	Chr4	27897600	27897620	20
Deletion	Chr4	28192256	28192257	1	LOC_Os04g47530
Deletion	Chr1	28872373	28874279	1906	LOC_Os01g50259
Deletion	Chr4	30951979	30951981	2	LOC_Os04g52110
Deletion	Chr4	33033011	33044918	11907	2
Deletion	Chr1	34200046	34200048	2
Deletion	Chr1	42574602	42574608	6

Insertions: 12

Variant Type	Chromosome	Start	End	Size (bp)
Insertion	Chr1	11509713	11509769	57
Insertion	Chr10	15535227	15535228	2
Insertion	Chr12	6065124	6065191	68
Insertion	Chr2	25733042	25733096	55
Insertion	Chr3	22012978	22012989	12
Insertion	Chr3	6553761	6553770	10
Insertion	Chr6	10243235	10243235	1
Insertion	Chr6	14883406	14883406	1
Insertion	Chr6	17918385	17918385	1
Insertion	Chr6	18896159	18896159	1
Insertion	Chr9	18370338	18370366	29
Insertion	Chr9	4781746	4781811	66

Inversions: 6

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr8	5037963	6933453
Inversion	Chr7	11686342	11745117	LOC_Os07g20270
Inversion	Chr10	13197353	16207573	LOC_Os10g31030
Inversion	Chr5	19097731	20289393	LOC_Os05g32610
Inversion	Chr1	25991732	27264933	LOC_Os01g47650
Inversion	Chr1	26002474	27264838	LOC_Os01g47650

Translocations: 9

Variant Type	Chromosome	Position 1	Chromosome	Position 2	Number of Genes
Translocation	Chr9	993875	Chr1	28874273	LOC_Os09g02400
Translocation	Chr9	993882	Chr1	28872373	2
Translocation	Chr9	2717453	Chr7	24948461	LOC_Os07g41610
Translocation	Chr10	9149132	Chr1	26012073
Translocation	Chr12	13386894	Chr6	13714514	LOC_Os06g23504
Translocation	Chr9	15061219	Chr4	29266248	LOC_Os09g25130
Translocation	Chr12	18797982	Chr3	20578516	LOC_Os03g37130
Translocation	Chr11	21132545	Chr7	11686355	LOC_Os07g20270
Translocation	Chr9	21144747	Chr1	25991766

Tandem duplications: 1

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Tandem Duplication	Chr2	16294367	16294367	0	LOC_Os02g27520

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