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Mutant Information

SOS indicates the sequenced line is sterile and seeds from siblings are available.

Mutant Name	FN552-S [Download]
Generation	M2-SOS
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN552-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: 34

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	15321121	G-T	HOMO	INTRON
SBS	Chr1	32913977	G-T	HET	NON_SYNONYMOUS_CODING	LOC_Os01g56980
SBS	Chr2	2086172	C-T	HET	INTERGENIC
SBS	Chr2	5887166	T-C	HOMO	INTERGENIC
SBS	Chr2	5887169	T-A	HOMO	INTERGENIC
SBS	Chr2	23896021	C-A	HET	INTRON
SBS	Chr3	965832	G-A	HET	INTERGENIC
SBS	Chr3	29934532	T-A	HOMO	INTERGENIC
SBS	Chr4	6710422	A-T	HET	INTRON
SBS	Chr4	31157438	C-A	HET	INTERGENIC
SBS	Chr5	8010857	G-T	HOMO	INTERGENIC
SBS	Chr5	14449526	G-A	HOMO	UTR_3_PRIME
SBS	Chr5	24398049	C-A	HET	NON_SYNONYMOUS_CODING	LOC_Os05g41700
SBS	Chr5	24398050	C-G	HET	SYNONYMOUS_CODING
SBS	Chr6	10774758	C-T	HET	NON_SYNONYMOUS_CODING	LOC_Os06g18950
SBS	Chr6	30352198	C-T	HOMO	INTERGENIC
SBS	Chr7	98242	G-A	HOMO	INTERGENIC
SBS	Chr7	6960847	G-T	HET	INTERGENIC
SBS	Chr7	9385948	G-A	HET	INTERGENIC
SBS	Chr7	10906465	C-A	HET	NON_SYNONYMOUS_CODING	LOC_Os07g18430
SBS	Chr7	10953197	A-T	HET	INTERGENIC
SBS	Chr7	26227125	C-T	HOMO	INTERGENIC
SBS	Chr8	4399717	T-A	HOMO	NON_SYNONYMOUS_CODING	LOC_Os08g07840
SBS	Chr8	27108401	A-G	HOMO	INTRON
SBS	Chr9	9236679	G-C	HOMO	INTERGENIC
SBS	Chr9	16235630	C-T	HET	INTERGENIC
SBS	Chr9	22313733	T-C	HET	SYNONYMOUS_CODING
SBS	Chr10	11118370	A-C	HET	INTERGENIC
SBS	Chr10	12407968	G-A	HET	SYNONYMOUS_CODING
SBS	Chr11	10667584	G-A	HOMO	STOP_GAINED	LOC_Os11g18790
SBS	Chr12	15721677	G-A	HET	INTRON
SBS	Chr12	22106686	G-A	HOMO	INTERGENIC
SBS	Chr12	25923464	A-T	HET	NON_SYNONYMOUS_CODING	LOC_Os12g41860
SBS	Chr12	25923465	G-T	HET	NON_SYNONYMOUS_CODING	LOC_Os12g41860

Deletions: 25

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Deletion	Chr3	341241	341242	1	LOC_Os03g01530
Deletion	Chr8	1095745	1095748	3
Deletion	Chr7	2253924	2253925	1
Deletion	Chr7	2629001	3292000	663000	101
Deletion	Chr1	4649043	4649055	12
Deletion	Chr9	4679934	4679936	2
Deletion	Chr10	5900330	5900332	2
Deletion	Chr7	6961529	6961530	1
Deletion	Chr4	7358536	7358547	11
Deletion	Chr4	9670374	9670377	3
Deletion	Chr4	9844994	9844999	5	LOC_Os04g17900
Deletion	Chr1	10990866	10990884	18	LOC_Os01g19430
Deletion	Chr6	12307939	12307940	1
Deletion	Chr7	16172683	16172684	1
Deletion	Chr2	16579031	16579034	3
Deletion	Chr10	21071398	21071399	1
Deletion	Chr5	21271121	21271122	1
Deletion	Chr7	22322722	22322723	1
Deletion	Chr6	22967305	22967314	9
Deletion	Chr8	23146456	23146457	1
Deletion	Chr2	23510158	23510170	12
Deletion	Chr5	24514493	24514496	3
Deletion	Chr8	26662131	26662144	13
Deletion	Chr4	34810564	34810565	1	LOC_Os04g58550
Deletion	Chr3	35343984	35343990	6

Insertions: 4

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Insertion	Chr7	11629690	11629703	14	LOC_Os07g20135
Insertion	Chr5	1778871	1778873	3
Insertion	Chr10	12437994	12437994	1
Insertion	Chr11	17850788	17850788	1

Inversions: 2

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr7	6058722	6949544	LOC_Os07g11010
Inversion	Chr7	6058735	6700741	LOC_Os07g11010

Translocations: 3

Variant Type	Chromosome	Position 1	Chromosome	Position 2	Number of Genes
Translocation	Chr11	6927454	Chr7	19968670	LOC_Os11g12410
Translocation	Chr4	11551033	Chr2	17320497
Translocation	Chr8	16362992	Chr4	18299491

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