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Mutant Information

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

Mutant Name	FN554-S [Download]
Generation	M2-SOS
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN554-S Alignment File
Seed Availability	Yes [Order Seeds]
Phenotype	TO:0000430 (Germination Rate) = Very Low (Below 24%) For more information, please see this phenotype file

Variant Information

Single base substitutions: 34

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 13200744 C-T Hetero INTERGENIC
SBS Chr1 19624871 C-A Hetero STOP_GAINED OsKitaake01g195600
SBS Chr1 26301429 C-T Hetero INTRON
SBS Chr1 30859934 A-T Homo UTR_3_PRIME
SBS Chr1 40419587 C-T Hetero INTERGENIC
SBS Chr2 2249052 A-T Hetero INTRON
SBS Chr3 15562971 A-G Hetero INTERGENIC
SBS Chr3 15702223 C-T Homo INTERGENIC
SBS Chr3 21270732 C-T Homo INTERGENIC
SBS Chr3 30786710 A-T Hetero INTERGENIC
SBS Chr4 1285211 T-A Homo INTERGENIC
SBS Chr4 13429400 T-C Hetero INTERGENIC
SBS Chr4 19518872 A-G Homo INTRON
SBS Chr4 35615195 T-C Hetero INTERGENIC
SBS Chr5 8939826 C-T Homo INTERGENIC
SBS Chr5 8939827 C-T Homo INTERGENIC
SBS Chr5 15723722 C-T Homo INTERGENIC
SBS Chr6 7187162 C-T Hetero INTERGENIC
SBS Chr7 14535096 C-T Homo INTERGENIC
SBS Chr7 16495641 G-A Homo INTERGENIC
SBS Chr7 16703602 T-C Homo INTRON
SBS Chr8 5825379 A-G Hetero INTERGENIC
SBS Chr8 9102312 A-T Hetero INTRON
SBS Chr8 9858094 A-T Hetero INTERGENIC
SBS Chr8 21324879 A-G Hetero INTERGENIC
SBS Chr9 3304024 T-C Hetero INTERGENIC
SBS Chr9 10252932 T-C Homo INTERGENIC
SBS Chr9 21007582 A-G Hetero INTRON
SBS Chr11 840636 A-G Hetero INTERGENIC
SBS Chr11 6951170 G-T Homo INTERGENIC
SBS Chr11 14174516 T-C Hetero INTERGENIC
SBS Chr12 10869978 T-C Homo INTERGENIC
SBS Chr12 18940426 C-A Hetero INTERGENIC
SBS Chr12 25066517 C-T Hetero NON_SYNONYMOUS_CODING OsKitaake12g203100

Deletions: 16

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr1 1589187 1589190 3
Deletion Chr7 3117294 3117419 125
Deletion Chr4 4036754 4036757 3 OsKitaake04g019650
Deletion Chr11 6348798 6348799 1 OsKitaake11g075700
Deletion Chr1 13222001 13291000 68999
Deletion Chr7 13227573 13227580 7
Deletion Chr7 13716001 13730000 13999
Deletion Chr7 16962044 16962051 7
Deletion Chr1 17029884 17029885 1
Deletion Chr7 18427349 18427360 11
Deletion Chr2 18700033 18700036 3
Deletion Chr12 19355193 19355197 4
Deletion Chr7 23500551 23500553 2
Deletion Chr5 23835789 23835791 2
Deletion Chr11 24591001 24599000 7999
Deletion Chr4 28816583 28816595 12

Insertions: 4

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr2 32643895 32643903 7
Insertion Chr5 29401543 29401546 2
Insertion Chr3 19362193 19362195 1
Insertion Chr4 31965684 31965686 1

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	13200744	C-T	Hetero	INTERGENIC
SBS	Chr1	19624871	C-A	Hetero	STOP_GAINED	OsKitaake01g195600
SBS	Chr1	26301429	C-T	Hetero	INTRON
SBS	Chr1	30859934	A-T	Homo	UTR_3_PRIME
SBS	Chr1	40419587	C-T	Hetero	INTERGENIC
SBS	Chr2	2249052	A-T	Hetero	INTRON
SBS	Chr3	15562971	A-G	Hetero	INTERGENIC
SBS	Chr3	15702223	C-T	Homo	INTERGENIC
SBS	Chr3	21270732	C-T	Homo	INTERGENIC
SBS	Chr3	30786710	A-T	Hetero	INTERGENIC
SBS	Chr4	1285211	T-A	Homo	INTERGENIC
SBS	Chr4	13429400	T-C	Hetero	INTERGENIC
SBS	Chr4	19518872	A-G	Homo	INTRON
SBS	Chr4	35615195	T-C	Hetero	INTERGENIC
SBS	Chr5	8939826	C-T	Homo	INTERGENIC
SBS	Chr5	8939827	C-T	Homo	INTERGENIC
SBS	Chr5	15723722	C-T	Homo	INTERGENIC
SBS	Chr6	7187162	C-T	Hetero	INTERGENIC
SBS	Chr7	14535096	C-T	Homo	INTERGENIC
SBS	Chr7	16495641	G-A	Homo	INTERGENIC
SBS	Chr7	16703602	T-C	Homo	INTRON
SBS	Chr8	5825379	A-G	Hetero	INTERGENIC
SBS	Chr8	9102312	A-T	Hetero	INTRON
SBS	Chr8	9858094	A-T	Hetero	INTERGENIC
SBS	Chr8	21324879	A-G	Hetero	INTERGENIC
SBS	Chr9	3304024	T-C	Hetero	INTERGENIC
SBS	Chr9	10252932	T-C	Homo	INTERGENIC
SBS	Chr9	21007582	A-G	Hetero	INTRON
SBS	Chr11	840636	A-G	Hetero	INTERGENIC
SBS	Chr11	6951170	G-T	Homo	INTERGENIC
SBS	Chr11	14174516	T-C	Hetero	INTERGENIC
SBS	Chr12	10869978	T-C	Homo	INTERGENIC
SBS	Chr12	18940426	C-A	Hetero	INTERGENIC
SBS	Chr12	25066517	C-T	Hetero	NON_SYNONYMOUS_CODING	OsKitaake12g203100

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr1	1589187	1589190	3
Deletion	Chr7	3117294	3117419	125
Deletion	Chr4	4036754	4036757	3	OsKitaake04g019650
Deletion	Chr11	6348798	6348799	1	OsKitaake11g075700
Deletion	Chr1	13222001	13291000	68999
Deletion	Chr7	13227573	13227580	7
Deletion	Chr7	13716001	13730000	13999
Deletion	Chr7	16962044	16962051	7
Deletion	Chr1	17029884	17029885	1
Deletion	Chr7	18427349	18427360	11
Deletion	Chr2	18700033	18700036	3
Deletion	Chr12	19355193	19355197	4
Deletion	Chr7	23500551	23500553	2
Deletion	Chr5	23835789	23835791	2
Deletion	Chr11	24591001	24599000	7999
Deletion	Chr4	28816583	28816595	12

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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