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Mutant Information

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

Mutant Name	FN-39 [Download]
Generation	M2-SOS
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN-39 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: 18

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 12970716 C-T Homo INTERGENIC
SBS Chr2 8172377 A-G Hetero UTR_3_PRIME
SBS Chr2 23606822 T-G Homo INTERGENIC
SBS Chr2 27801058 T-C Hetero NON_SYNONYMOUS_CODING OsKitaake02g279500
SBS Chr3 16284840 G-A Homo SYNONYMOUS_CODING
SBS Chr3 33264051 A-T Homo INTERGENIC
SBS Chr7 23394757 T-A Homo INTERGENIC
SBS Chr8 9993264 A-T Hetero INTERGENIC
SBS Chr8 10172005 G-A Hetero INTERGENIC
SBS Chr8 14506791 G-T Hetero INTERGENIC
SBS Chr8 21584881 C-G Hetero INTERGENIC
SBS Chr8 27749657 T-A Hetero INTRON
SBS Chr9 3697125 A-G Homo INTERGENIC
SBS Chr9 15322778 A-G Hetero UTR_3_PRIME
SBS Chr9 16666365 A-G Homo INTERGENIC
SBS Chr11 10477359 G-A Homo INTERGENIC
SBS Chr11 23074204 C-T Homo INTERGENIC
SBS Chr12 13247653 C-A Hetero INTERGENIC

Deletions: 15

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr11 5247690 5247699 9
Deletion Chr8 5290056 5290058 2
Deletion Chr11 5911507 5911508 1
Deletion Chr10 8675813 8675979 166
Deletion Chr4 8774078 8774083 5
Deletion Chr3 9827531 9827535 4 OsKitaake03g133900
Deletion Chr2 11898963 11898967 4
Deletion Chr11 14510127 14510498 371
Deletion Chr12 15184513 15184516 3
Deletion Chr11 15772498 15772502 4
Deletion Chr4 21968310 21968313 3 OsKitaake04g127600
Deletion Chr12 22048771 22048777 6
Deletion Chr10 23722653 23722659 6
Deletion Chr11 26476918 26476924 6
Deletion Chr1 35407972 35407977 5

Insertions: 2

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr5 15424490 15424492 1 OsKitaake05g118300
Insertion Chr11 12508912 12508914 1

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	12970716	C-T	Homo	INTERGENIC
SBS	Chr2	8172377	A-G	Hetero	UTR_3_PRIME
SBS	Chr2	23606822	T-G	Homo	INTERGENIC
SBS	Chr2	27801058	T-C	Hetero	NON_SYNONYMOUS_CODING	OsKitaake02g279500
SBS	Chr3	16284840	G-A	Homo	SYNONYMOUS_CODING
SBS	Chr3	33264051	A-T	Homo	INTERGENIC
SBS	Chr7	23394757	T-A	Homo	INTERGENIC
SBS	Chr8	9993264	A-T	Hetero	INTERGENIC
SBS	Chr8	10172005	G-A	Hetero	INTERGENIC
SBS	Chr8	14506791	G-T	Hetero	INTERGENIC
SBS	Chr8	21584881	C-G	Hetero	INTERGENIC
SBS	Chr8	27749657	T-A	Hetero	INTRON
SBS	Chr9	3697125	A-G	Homo	INTERGENIC
SBS	Chr9	15322778	A-G	Hetero	UTR_3_PRIME
SBS	Chr9	16666365	A-G	Homo	INTERGENIC
SBS	Chr11	10477359	G-A	Homo	INTERGENIC
SBS	Chr11	23074204	C-T	Homo	INTERGENIC
SBS	Chr12	13247653	C-A	Hetero	INTERGENIC

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr11	5247690	5247699	9
Deletion	Chr8	5290056	5290058	2
Deletion	Chr11	5911507	5911508	1
Deletion	Chr10	8675813	8675979	166
Deletion	Chr4	8774078	8774083	5
Deletion	Chr3	9827531	9827535	4	OsKitaake03g133900
Deletion	Chr2	11898963	11898967	4
Deletion	Chr11	14510127	14510498	371
Deletion	Chr12	15184513	15184516	3
Deletion	Chr11	15772498	15772502	4
Deletion	Chr4	21968310	21968313	3	OsKitaake04g127600
Deletion	Chr12	22048771	22048777	6
Deletion	Chr10	23722653	23722659	6
Deletion	Chr11	26476918	26476924	6
Deletion	Chr1	35407972	35407977	5

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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