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Mutant Information

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

Mutant Name	FN-50 [Download]
Generation	M2-SOS
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN-50 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

Variant Information

Single base substitutions: 36

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 10620131 G-A Hetero INTERGENIC
SBS Chr1 20033838 G-T Homo INTERGENIC
SBS Chr2 13964286 G-A Hetero INTERGENIC
SBS Chr2 17270640 T-G Hetero INTERGENIC
SBS Chr2 19650081 C-A Hetero INTERGENIC
SBS Chr2 21000733 T-C Hetero INTERGENIC
SBS Chr2 21602571 T-C Hetero INTERGENIC
SBS Chr3 1569167 T-C Homo INTRON
SBS Chr3 6165550 T-C Hetero INTERGENIC
SBS Chr3 11713928 A-G Hetero INTRON
SBS Chr3 21907986 C-T Hetero INTERGENIC
SBS Chr3 24187046 T-C Hetero NON_SYNONYMOUS_CODING OsKitaake03g258300
SBS Chr4 4833225 C-A Hetero INTERGENIC
SBS Chr4 4833226 C-A Hetero INTERGENIC
SBS Chr4 9045553 G-A Homo INTERGENIC
SBS Chr4 16516877 C-T Hetero INTERGENIC
SBS Chr4 20701374 A-G Hetero INTERGENIC
SBS Chr4 25443219 C-T Hetero INTRON
SBS Chr5 14796090 A-T Hetero INTERGENIC
SBS Chr5 16096809 A-T Hetero INTERGENIC
SBS Chr5 21260170 T-C Homo INTRON
SBS Chr6 7083660 T-C Hetero INTERGENIC
SBS Chr6 22537501 T-G Hetero INTERGENIC
SBS Chr7 24077836 T-C Hetero INTERGENIC
SBS Chr8 8383806 T-G Homo UTR_3_PRIME
SBS Chr8 24466601 C-T Hetero INTRON
SBS Chr8 26619529 A-T Hetero INTERGENIC
SBS Chr9 15725977 T-C Homo INTERGENIC
SBS Chr9 17743454 C-T Homo INTRON
SBS Chr10 18802310 A-T Homo NON_SYNONYMOUS_CODING OsKitaake10g134000
SBS Chr11 24116895 A-T Homo INTERGENIC
SBS Chr12 11134910 A-C Homo INTERGENIC
SBS Chr12 22283537 A-C Homo INTERGENIC
SBS Chr12 23374820 A-T Homo INTRON
SBS Chr12 24861060 T-C Hetero INTERGENIC
SBS Chr12 26773530 T-G Hetero INTERGENIC

Deletions: 13

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr4 9226001 9614000 387999 16
Deletion Chr2 11722001 11735000 12999
Deletion Chr7 13286623 13286628 5
Deletion Chr9 14176471 14176472 1
Deletion Chr12 15184513 15184516 3
Deletion Chr6 15442384 15442386 2
Deletion Chr4 15864378 15864380 2 OsKitaake04g077550
Deletion Chr11 19008402 19008406 4
Deletion Chr1 23646393 23646512 119
Deletion Chr1 31225271 31225275 4
Deletion Chr1 32146833 32146834 1
Deletion Chr3 34097558 34097579 21
Deletion Chr3 34677897 34677898 1 OsKitaake03g377400

Insertions: 2

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr2 27539645 27539648 2
Insertion Chr4 4414990 4414992 1

Inversions: 1

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Inversion Chr2 12854449 13325031

Translocations: 2

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes

Translocation Chr6 219121 Chr5 25797635 OsKitaake06g001200
Translocation Chr6 224096 Chr5 25797601 OsKitaake06g001200

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	10620131	G-A	Hetero	INTERGENIC
SBS	Chr1	20033838	G-T	Homo	INTERGENIC
SBS	Chr2	13964286	G-A	Hetero	INTERGENIC
SBS	Chr2	17270640	T-G	Hetero	INTERGENIC
SBS	Chr2	19650081	C-A	Hetero	INTERGENIC
SBS	Chr2	21000733	T-C	Hetero	INTERGENIC
SBS	Chr2	21602571	T-C	Hetero	INTERGENIC
SBS	Chr3	1569167	T-C	Homo	INTRON
SBS	Chr3	6165550	T-C	Hetero	INTERGENIC
SBS	Chr3	11713928	A-G	Hetero	INTRON
SBS	Chr3	21907986	C-T	Hetero	INTERGENIC
SBS	Chr3	24187046	T-C	Hetero	NON_SYNONYMOUS_CODING	OsKitaake03g258300
SBS	Chr4	4833225	C-A	Hetero	INTERGENIC
SBS	Chr4	4833226	C-A	Hetero	INTERGENIC
SBS	Chr4	9045553	G-A	Homo	INTERGENIC
SBS	Chr4	16516877	C-T	Hetero	INTERGENIC
SBS	Chr4	20701374	A-G	Hetero	INTERGENIC
SBS	Chr4	25443219	C-T	Hetero	INTRON
SBS	Chr5	14796090	A-T	Hetero	INTERGENIC
SBS	Chr5	16096809	A-T	Hetero	INTERGENIC
SBS	Chr5	21260170	T-C	Homo	INTRON
SBS	Chr6	7083660	T-C	Hetero	INTERGENIC
SBS	Chr6	22537501	T-G	Hetero	INTERGENIC
SBS	Chr7	24077836	T-C	Hetero	INTERGENIC
SBS	Chr8	8383806	T-G	Homo	UTR_3_PRIME
SBS	Chr8	24466601	C-T	Hetero	INTRON
SBS	Chr8	26619529	A-T	Hetero	INTERGENIC
SBS	Chr9	15725977	T-C	Homo	INTERGENIC
SBS	Chr9	17743454	C-T	Homo	INTRON
SBS	Chr10	18802310	A-T	Homo	NON_SYNONYMOUS_CODING	OsKitaake10g134000
SBS	Chr11	24116895	A-T	Homo	INTERGENIC
SBS	Chr12	11134910	A-C	Homo	INTERGENIC
SBS	Chr12	22283537	A-C	Homo	INTERGENIC
SBS	Chr12	23374820	A-T	Homo	INTRON
SBS	Chr12	24861060	T-C	Hetero	INTERGENIC
SBS	Chr12	26773530	T-G	Hetero	INTERGENIC

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr4	9226001	9614000	387999	16
Deletion	Chr2	11722001	11735000	12999
Deletion	Chr7	13286623	13286628	5
Deletion	Chr9	14176471	14176472	1
Deletion	Chr12	15184513	15184516	3
Deletion	Chr6	15442384	15442386	2
Deletion	Chr4	15864378	15864380	2	OsKitaake04g077550
Deletion	Chr11	19008402	19008406	4
Deletion	Chr1	23646393	23646512	119
Deletion	Chr1	31225271	31225275	4
Deletion	Chr1	32146833	32146834	1
Deletion	Chr3	34097558	34097579	21
Deletion	Chr3	34677897	34677898	1	OsKitaake03g377400

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr2	12854449	13325031

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Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes