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Mutant Information

Mutant Name	FN1278-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN1278-S Alignment File
Seed Availability	Yes [Order Seeds]
Phenotype	TO:0000014 (Panicle Weight) = Low (Between 25% and 74%) TO:0000207 (Plant height) = Normal (Between 75% and 125%) TO:0000445 (Seed Number) = Low (Between 25% and 74%) TO:0000639 (Seed fertility) = Normal (Between 75% and 125%) For more information, please see this phenotype file

Variant Information

Single base substitutions: 51

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 3048522 T-A Homo INTERGENIC
SBS Chr1 6098226 C-T Homo INTERGENIC
SBS Chr1 11789526 C-A Hetero INTERGENIC
SBS Chr1 13447310 A-T Hetero INTERGENIC
SBS Chr1 18866909 G-A Homo INTERGENIC
SBS Chr1 19946518 G-A Homo INTERGENIC
SBS Chr1 35064066 T-A Hetero INTERGENIC
SBS Chr1 35064067 T-A Hetero INTERGENIC
SBS Chr1 42087638 G-A Hetero INTERGENIC
SBS Chr2 6670141 A-T Homo INTRON
SBS Chr2 17402758 A-G Homo INTERGENIC
SBS Chr2 17403132 A-G Homo INTERGENIC
SBS Chr2 24038037 G-A Hetero INTERGENIC
SBS Chr2 31047589 C-G Hetero INTERGENIC
SBS Chr3 4966232 T-C Hetero INTRON
SBS Chr3 17195019 C-A Hetero INTERGENIC
SBS Chr3 21652981 C-G Hetero INTERGENIC
SBS Chr3 25770819 T-C Hetero INTERGENIC
SBS Chr4 12492785 T-C Homo INTERGENIC
SBS Chr4 13970927 G-T Homo SYNONYMOUS_CODING
SBS Chr4 15736032 A-T Homo INTERGENIC
SBS Chr4 27547971 C-T Homo INTERGENIC
SBS Chr5 1302054 C-T Hetero INTERGENIC
SBS Chr5 5390514 A-G Homo INTERGENIC
SBS Chr5 13635048 T-C Homo INTERGENIC
SBS Chr6 13240647 G-T Hetero INTERGENIC
SBS Chr6 13429353 C-A Hetero INTERGENIC
SBS Chr6 14079580 G-A Homo INTERGENIC
SBS Chr6 17600213 C-G Hetero INTERGENIC
SBS Chr6 27377591 A-G Homo SYNONYMOUS_CODING
SBS Chr7 11570950 G-T Hetero INTERGENIC
SBS Chr8 15604638 C-T Homo INTERGENIC
SBS Chr9 4783705 A-G Homo INTERGENIC
SBS Chr9 5161229 T-C Homo INTERGENIC
SBS Chr9 8167437 C-G Homo INTERGENIC
SBS Chr10 9552062 G-A Hetero INTRON
SBS Chr10 14097380 T-C Homo INTERGENIC
SBS Chr10 23881683 A-T Hetero SPLICE_SITE_REGION
SBS Chr10 23881684 C-A Hetero SPLICE_SITE_REGION
SBS Chr11 5178008 G-A Homo INTERGENIC
SBS Chr11 6378745 A-C Hetero INTERGENIC
SBS Chr11 9631296 G-A Hetero INTERGENIC
SBS Chr11 10049354 G-A Hetero INTERGENIC
SBS Chr11 10049356 G-A Hetero INTERGENIC
SBS Chr11 10049359 T-A Hetero INTERGENIC
SBS Chr12 6004586 C-T Hetero INTERGENIC
SBS Chr12 7689462 G-T Hetero INTERGENIC
SBS Chr12 8569215 A-C Hetero INTERGENIC
SBS Chr12 17577746 G-T Hetero INTERGENIC
SBS Chr12 22557985 T-C Homo INTERGENIC
SBS Chr12 26459443 T-C Homo INTERGENIC

Deletions: 16

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr10 224733 224736 3
Deletion Chr9 264733 264743 10
Deletion Chr4 8893760 8893771 11
Deletion Chr10 10716339 10716350 11
Deletion Chr8 11256396 11256399 3
Deletion Chr11 12019664 12019665 1
Deletion Chr1 14339001 14415000 75999 6
Deletion Chr1 14417001 14502000 84999 6
Deletion Chr2 18152222 18152231 9 OsKitaake02g180600
Deletion Chr4 20147662 20147670 8
Deletion Chr8 21833632 21833634 2
Deletion Chr8 22514924 22514930 6
Deletion Chr3 24214773 24214780 7
Deletion Chr3 25782103 25782105 2
Deletion Chr7 27207690 27207695 5
Deletion Chr2 34130663 34130671 8

Insertions: 3

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr2 36329726 36329734 7
Insertion Chr7 19402677 19402679 1
Insertion Chr9 2754472 2754474 1

Translocations: 5

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes

Translocation Chr6 15054068 Chr3 5280688
Translocation Chr6 15055005 Chr3 5280644
Translocation Chr11 22789669 Chr3 5280643 OsKitaake11g180700
Translocation Chr3 30149195 Chr2 36554249 OsKitaake02g388700
Translocation Chr3 30149209 Chr2 36551151 OsKitaake02g388700

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	3048522	T-A	Homo	INTERGENIC
SBS	Chr1	6098226	C-T	Homo	INTERGENIC
SBS	Chr1	11789526	C-A	Hetero	INTERGENIC
SBS	Chr1	13447310	A-T	Hetero	INTERGENIC
SBS	Chr1	18866909	G-A	Homo	INTERGENIC
SBS	Chr1	19946518	G-A	Homo	INTERGENIC
SBS	Chr1	35064066	T-A	Hetero	INTERGENIC
SBS	Chr1	35064067	T-A	Hetero	INTERGENIC
SBS	Chr1	42087638	G-A	Hetero	INTERGENIC
SBS	Chr2	6670141	A-T	Homo	INTRON
SBS	Chr2	17402758	A-G	Homo	INTERGENIC
SBS	Chr2	17403132	A-G	Homo	INTERGENIC
SBS	Chr2	24038037	G-A	Hetero	INTERGENIC
SBS	Chr2	31047589	C-G	Hetero	INTERGENIC
SBS	Chr3	4966232	T-C	Hetero	INTRON
SBS	Chr3	17195019	C-A	Hetero	INTERGENIC
SBS	Chr3	21652981	C-G	Hetero	INTERGENIC
SBS	Chr3	25770819	T-C	Hetero	INTERGENIC
SBS	Chr4	12492785	T-C	Homo	INTERGENIC
SBS	Chr4	13970927	G-T	Homo	SYNONYMOUS_CODING
SBS	Chr4	15736032	A-T	Homo	INTERGENIC
SBS	Chr4	27547971	C-T	Homo	INTERGENIC
SBS	Chr5	1302054	C-T	Hetero	INTERGENIC
SBS	Chr5	5390514	A-G	Homo	INTERGENIC
SBS	Chr5	13635048	T-C	Homo	INTERGENIC
SBS	Chr6	13240647	G-T	Hetero	INTERGENIC
SBS	Chr6	13429353	C-A	Hetero	INTERGENIC
SBS	Chr6	14079580	G-A	Homo	INTERGENIC
SBS	Chr6	17600213	C-G	Hetero	INTERGENIC
SBS	Chr6	27377591	A-G	Homo	SYNONYMOUS_CODING
SBS	Chr7	11570950	G-T	Hetero	INTERGENIC
SBS	Chr8	15604638	C-T	Homo	INTERGENIC
SBS	Chr9	4783705	A-G	Homo	INTERGENIC
SBS	Chr9	5161229	T-C	Homo	INTERGENIC
SBS	Chr9	8167437	C-G	Homo	INTERGENIC
SBS	Chr10	9552062	G-A	Hetero	INTRON
SBS	Chr10	14097380	T-C	Homo	INTERGENIC
SBS	Chr10	23881683	A-T	Hetero	SPLICE_SITE_REGION
SBS	Chr10	23881684	C-A	Hetero	SPLICE_SITE_REGION
SBS	Chr11	5178008	G-A	Homo	INTERGENIC
SBS	Chr11	6378745	A-C	Hetero	INTERGENIC
SBS	Chr11	9631296	G-A	Hetero	INTERGENIC
SBS	Chr11	10049354	G-A	Hetero	INTERGENIC
SBS	Chr11	10049356	G-A	Hetero	INTERGENIC
SBS	Chr11	10049359	T-A	Hetero	INTERGENIC
SBS	Chr12	6004586	C-T	Hetero	INTERGENIC
SBS	Chr12	7689462	G-T	Hetero	INTERGENIC
SBS	Chr12	8569215	A-C	Hetero	INTERGENIC
SBS	Chr12	17577746	G-T	Hetero	INTERGENIC
SBS	Chr12	22557985	T-C	Homo	INTERGENIC
SBS	Chr12	26459443	T-C	Homo	INTERGENIC

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr10	224733	224736	3
Deletion	Chr9	264733	264743	10
Deletion	Chr4	8893760	8893771	11
Deletion	Chr10	10716339	10716350	11
Deletion	Chr8	11256396	11256399	3
Deletion	Chr11	12019664	12019665	1
Deletion	Chr1	14339001	14415000	75999	6
Deletion	Chr1	14417001	14502000	84999	6
Deletion	Chr2	18152222	18152231	9	OsKitaake02g180600
Deletion	Chr4	20147662	20147670	8
Deletion	Chr8	21833632	21833634	2
Deletion	Chr8	22514924	22514930	6
Deletion	Chr3	24214773	24214780	7
Deletion	Chr3	25782103	25782105	2
Deletion	Chr7	27207690	27207695	5
Deletion	Chr2	34130663	34130671	8

Variant Type	Chromosome	Position 1	Chromosome	Position 2	Number of Genes
Translocation	Chr6	15054068	Chr3	5280688
Translocation	Chr6	15055005	Chr3	5280644
Translocation	Chr11	22789669	Chr3	5280643	OsKitaake11g180700
Translocation	Chr3	30149195	Chr2	36554249	OsKitaake02g388700
Translocation	Chr3	30149209	Chr2	36551151	OsKitaake02g388700

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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

Chromosome

Position 2

Number of Genes