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Mutant Information

Mutant Name	FN1400-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN1400-S Alignment File
Seed Availability	Yes [Order Seeds]
Phenotype	TO:0000326 (Leaf Color) = Normal TO:0000137 (Days to heading) = Normal (Between 75% and 125%) TO:0000346 (Tiller number) = High (Between 126% and 175%) TO:0000430 (Germination Rate) = Low (Between 25% and 75%) For more information, please see this phenotype file

Variant Information

Single base substitutions: 30

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 12957809 G-A Homo INTERGENIC
SBS Chr1 14928486 C-T Homo INTERGENIC
SBS Chr1 23489083 C-T Hetero INTERGENIC
SBS Chr1 26118801 C-A Hetero INTERGENIC
SBS Chr1 26118808 G-T Hetero INTERGENIC
SBS Chr2 14572605 G-A Homo INTERGENIC
SBS Chr2 31950821 A-G Hetero INTERGENIC
SBS Chr2 33385108 A-G Hetero INTERGENIC
SBS Chr2 36031906 C-T Hetero INTERGENIC
SBS Chr3 16164228 G-T Homo NON_SYNONYMOUS_CODING OsKitaake03g206100
SBS Chr3 16164229 G-T Homo SYNONYMOUS_CODING
SBS Chr5 7789878 C-A Hetero INTRON
SBS Chr5 15354590 G-A Homo INTERGENIC
SBS Chr5 16162127 C-A Hetero INTERGENIC
SBS Chr7 557613 C-A Hetero INTERGENIC
SBS Chr7 13249831 C-T Hetero INTERGENIC
SBS Chr8 15485107 C-T Hetero INTERGENIC
SBS Chr8 15825044 A-T Hetero INTERGENIC
SBS Chr8 15825046 G-T Hetero INTERGENIC
SBS Chr9 16773955 T-C Homo INTERGENIC
SBS Chr10 14033226 C-A Homo INTRON
SBS Chr10 17676148 C-T Hetero INTERGENIC
SBS Chr10 20388273 G-A Homo SYNONYMOUS_CODING
SBS Chr11 3306878 C-T Hetero INTERGENIC
SBS Chr11 8630721 C-A Homo INTERGENIC
SBS Chr11 21200639 G-A Hetero INTERGENIC
SBS Chr12 6191211 G-T Homo INTERGENIC
SBS Chr12 15749673 C-T Hetero INTERGENIC
SBS Chr12 15749678 A-G Hetero INTERGENIC
SBS Chr12 16099987 G-A Hetero INTERGENIC

Deletions: 11

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr5 1368001 1381000 12999 OsKitaake05g017100
Deletion Chr4 9527528 9527531 3
Deletion Chr3 9638185 9638189 4
Deletion Chr1 9644001 9660000 15999 OsKitaake01g123400
Deletion Chr1 10116955 10116956 1
Deletion Chr7 11075001 11087000 11999 OsKitaake07g104332
Deletion Chr3 11603840 11603843 3 OsKitaake03g157700
Deletion Chr3 22397344 22397349 5
Deletion Chr8 23471001 23587000 115999 8
Deletion Chr5 29633001 29644000 10999 3
Deletion Chr3 35337001 35343000 5999 OsKitaake03g387600

Insertions: 8

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr1 10036997 10037000 2
Insertion Chr1 42131947 42131950 2
Insertion Chr2 14475430 14475433 2
Insertion Chr9 2709795 2709798 2
Insertion Chr9 12117705 12117708 2
Insertion Chr11 11424477 11424485 7
Insertion Chr12 17566882 17566887 4
Insertion Chr6 7838 7840 1

Translocations: 6

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes

Translocation Chr9 4495244 Chr8 15816860 OsKitaake09g025500
Translocation Chr9 4495255 Chr8 15817235 OsKitaake09g025500
Translocation Chr8 12849988 Chr3 36808116 OsKitaake03g410800
Translocation Chr8 12850355 Chr3 36798208 OsKitaake03g410600
Translocation Chr5 29632970 Chr1 1434960
Translocation Chr5 29643254 Chr1 1434084

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	12957809	G-A	Homo	INTERGENIC
SBS	Chr1	14928486	C-T	Homo	INTERGENIC
SBS	Chr1	23489083	C-T	Hetero	INTERGENIC
SBS	Chr1	26118801	C-A	Hetero	INTERGENIC
SBS	Chr1	26118808	G-T	Hetero	INTERGENIC
SBS	Chr2	14572605	G-A	Homo	INTERGENIC
SBS	Chr2	31950821	A-G	Hetero	INTERGENIC
SBS	Chr2	33385108	A-G	Hetero	INTERGENIC
SBS	Chr2	36031906	C-T	Hetero	INTERGENIC
SBS	Chr3	16164228	G-T	Homo	NON_SYNONYMOUS_CODING	OsKitaake03g206100
SBS	Chr3	16164229	G-T	Homo	SYNONYMOUS_CODING
SBS	Chr5	7789878	C-A	Hetero	INTRON
SBS	Chr5	15354590	G-A	Homo	INTERGENIC
SBS	Chr5	16162127	C-A	Hetero	INTERGENIC
SBS	Chr7	557613	C-A	Hetero	INTERGENIC
SBS	Chr7	13249831	C-T	Hetero	INTERGENIC
SBS	Chr8	15485107	C-T	Hetero	INTERGENIC
SBS	Chr8	15825044	A-T	Hetero	INTERGENIC
SBS	Chr8	15825046	G-T	Hetero	INTERGENIC
SBS	Chr9	16773955	T-C	Homo	INTERGENIC
SBS	Chr10	14033226	C-A	Homo	INTRON
SBS	Chr10	17676148	C-T	Hetero	INTERGENIC
SBS	Chr10	20388273	G-A	Homo	SYNONYMOUS_CODING
SBS	Chr11	3306878	C-T	Hetero	INTERGENIC
SBS	Chr11	8630721	C-A	Homo	INTERGENIC
SBS	Chr11	21200639	G-A	Hetero	INTERGENIC
SBS	Chr12	6191211	G-T	Homo	INTERGENIC
SBS	Chr12	15749673	C-T	Hetero	INTERGENIC
SBS	Chr12	15749678	A-G	Hetero	INTERGENIC
SBS	Chr12	16099987	G-A	Hetero	INTERGENIC

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr5	1368001	1381000	12999	OsKitaake05g017100
Deletion	Chr4	9527528	9527531	3
Deletion	Chr3	9638185	9638189	4
Deletion	Chr1	9644001	9660000	15999	OsKitaake01g123400
Deletion	Chr1	10116955	10116956	1
Deletion	Chr7	11075001	11087000	11999	OsKitaake07g104332
Deletion	Chr3	11603840	11603843	3	OsKitaake03g157700
Deletion	Chr3	22397344	22397349	5
Deletion	Chr8	23471001	23587000	115999	8
Deletion	Chr5	29633001	29644000	10999	3
Deletion	Chr3	35337001	35343000	5999	OsKitaake03g387600

Variant Type	Chromosome	Position 1	Chromosome	Position 2	Number of Genes
Translocation	Chr9	4495244	Chr8	15816860	OsKitaake09g025500
Translocation	Chr9	4495255	Chr8	15817235	OsKitaake09g025500
Translocation	Chr8	12849988	Chr3	36808116	OsKitaake03g410800
Translocation	Chr8	12850355	Chr3	36798208	OsKitaake03g410600
Translocation	Chr5	29632970	Chr1	1434960
Translocation	Chr5	29643254	Chr1	1434084

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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