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Mutant Information

Mutant Name	FN1309-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN1309-S Alignment File
Seed Availability	Yes [Order Seeds]
Phenotype	TO:0000326 (Leaf Color) = Normal TO:0000137 (Days to heading) = Normal (Between 75% and 125%) TO:0000346 (Tiller number) = Low (Between 25% and 74%) 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: 35

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	10422438	A-T	HET	INTERGENIC
SBS	Chr1	19667889	G-C	HOMO	INTRON
SBS	Chr1	20276279	T-A	HOMO	STOP_GAINED	LOC_Os01g36530
SBS	Chr1	2549447	G-A	HET	INTERGENIC
SBS	Chr1	28967699	C-T	HET	INTERGENIC
SBS	Chr10	1038640	T-C	HOMO	INTERGENIC
SBS	Chr11	16375193	G-A	HET	NON_SYNONYMOUS_CODING	LOC_Os11g28440
SBS	Chr11	18836550	C-T	HOMO	INTERGENIC
SBS	Chr11	3733354	C-A	HOMO	INTERGENIC
SBS	Chr11	7013142	A-C	HET	NON_SYNONYMOUS_CODING	LOC_Os11g12530
SBS	Chr12	17329774	G-A	HET	INTERGENIC
SBS	Chr12	19421957	C-T	HOMO	INTERGENIC
SBS	Chr2	23390089	C-A	HOMO	NON_SYNONYMOUS_CODING	LOC_Os02g38690
SBS	Chr2	4504653	G-T	HET	INTERGENIC
SBS	Chr2	5311527	T-G	HET	INTERGENIC
SBS	Chr2	6144154	C-T	HET	INTERGENIC
SBS	Chr3	10339655	G-A	HOMO	INTERGENIC
SBS	Chr3	10339656	A-G	HOMO	INTERGENIC
SBS	Chr3	27775109	G-C	HET	INTERGENIC
SBS	Chr3	6314468	C-T	HOMO	INTERGENIC
SBS	Chr3	9389132	C-A	HET	INTERGENIC
SBS	Chr4	1032239	C-T	HET	SYNONYMOUS_CODING
SBS	Chr4	10345128	C-T	HET	INTERGENIC
SBS	Chr4	1115679	T-C	HOMO	INTRON
SBS	Chr5	14429626	G-A	HET	INTRON
SBS	Chr5	16891825	A-T	HET	INTRON
SBS	Chr5	7892642	G-A	HET	INTERGENIC
SBS	Chr6	22108473	T-G	HET	NON_SYNONYMOUS_CODING	LOC_Os06g37400
SBS	Chr6	8748807	C-T	HET	INTERGENIC
SBS	Chr7	12855067	G-T	HOMO	INTERGENIC
SBS	Chr7	5095591	C-A	HOMO	INTERGENIC
SBS	Chr8	19995242	A-G	HET	INTRON
SBS	Chr8	474147	A-G	HOMO	INTERGENIC
SBS	Chr9	19014733	C-T	HET	INTERGENIC
SBS	Chr9	3616042	G-A	HOMO	INTERGENIC

Deletions: 21

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Deletion	Chr12	6948413	6948426	13
Deletion	Chr5	7321116	7321129	13
Deletion	Chr3	10336214	10336257	43	LOC_Os03g18430
Deletion	Chr5	10885644	10885686	42	LOC_Os05g18770
Deletion	Chr4	11914447	11914448	1
Deletion	Chr3	12314931	12314934	3
Deletion	Chr6	12535460	12535461	1
Deletion	Chr4	13383336	13383340	4
Deletion	Chr7	13779058	13779069	11
Deletion	Chr1	13847138	13847139	1
Deletion	Chr6	16137363	16137374	11
Deletion	Chr8	17459178	17459196	18
Deletion	Chr8	19223228	19223234	6	LOC_Os08g31130
Deletion	Chr5	20062225	20062228	3	LOC_Os05g33980
Deletion	Chr3	20208150	20208159	9
Deletion	Chr4	20313319	20313322	3
Deletion	Chr8	23676640	23676644	4
Deletion	Chr6	24491076	24491079	3
Deletion	Chr1	25493635	25493636	1
Deletion	Chr4	25926429	25926441	12
Deletion	Chr3	33811482	33811485	3

Insertions: 3

Variant Type	Chromosome	Start	End	Size (bp)
Insertion	Chr1	11052183	11052184	2
Insertion	Chr11	1878359	1878360	2
Insertion	Chr5	49552	49553	2

Inversions: 5

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr6	12292645	13288458	LOC_Os06g21260
Inversion	Chr6	12297726	13288459
Inversion	Chr7	15159329	15667779
Inversion	Chr1	19264221	19645709	LOC_Os01g35504
Inversion	Chr3	36140513	36229621	LOC_Os03g64110

Translocations: 4

Variant Type	Chromosome	Position 1	Chromosome	Position 2	Number of Genes
Translocation	Chr7	20745755	Chr2	15495233	LOC_Os07g34598
Translocation	Chr8	23824300	Chr7	20745764	2
Translocation	Chr11	26515493	Chr8	23824337	LOC_Os08g37600
Translocation	Chr11	26517206	Chr8	23824961	LOC_Os08g37600

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