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Mutant Information

Mutant Name	FN-4 [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN-4 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) = Low (Between 25% and 74%) For more information, please see this phenotype file

Variant Information

Single base substitutions: 21

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr3 9143233 G-A Hetero UTR_3_PRIME
SBS Chr3 17671413 C-T Hetero INTERGENIC
SBS Chr3 18426579 T-A Hetero INTERGENIC
SBS Chr3 19564587 T-C Hetero INTERGENIC
SBS Chr3 34373736 T-G Hetero INTERGENIC
SBS Chr3 37483445 G-T Hetero INTERGENIC
SBS Chr4 3124376 A-G Homo INTERGENIC
SBS Chr4 5669983 G-A Homo INTERGENIC
SBS Chr4 14094394 G-A Hetero INTERGENIC
SBS Chr4 14815159 A-T Hetero INTERGENIC
SBS Chr5 7151201 A-T Homo INTERGENIC
SBS Chr7 29552456 T-A Hetero INTRON
SBS Chr8 11606221 C-T Hetero INTERGENIC
SBS Chr8 17827458 A-G Homo INTERGENIC
SBS Chr9 21735003 A-C Hetero INTRON
SBS Chr11 2542788 T-G Hetero INTERGENIC
SBS Chr11 14413901 C-A Homo INTERGENIC
SBS Chr11 20644444 C-T Homo INTERGENIC
SBS Chr12 13098879 C-T Homo INTERGENIC
SBS Chr12 23906510 C-G Homo INTRON
SBS Chr12 24497362 G-A Homo NON_SYNONYMOUS_CODING OsKitaake12g197600

Deletions: 14

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr4 5670586 5670587 1
Deletion Chr12 6593001 6800000 206999 14
Deletion Chr8 7797980 7797990 10
Deletion Chr6 9057160 9057166 6
Deletion Chr10 9848556 9848558 2
Deletion Chr11 13701211 13701220 9
Deletion Chr10 13984628 13984699 71
Deletion Chr9 19998061 19998062 1
Deletion Chr10 20452763 20452764 1 OsKitaake10g156500
Deletion Chr8 21906253 21906258 5
Deletion Chr6 22869946 22869947 1
Deletion Chr1 23291001 23400000 108999 11
Deletion Chr8 27690724 27690725 1
Deletion Chr5 30121645 30121646 1

Insertions: 3

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr1 43241577 43241580 2
Insertion Chr3 20050183 20050185 1
Insertion Chr4 16857457 16857459 1

Translocations: 2

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes

Translocation Chr12 1303552 Chr1 457927 2
Translocation Chr12 1304408 Chr1 457920 2

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr3	9143233	G-A	Hetero	UTR_3_PRIME
SBS	Chr3	17671413	C-T	Hetero	INTERGENIC
SBS	Chr3	18426579	T-A	Hetero	INTERGENIC
SBS	Chr3	19564587	T-C	Hetero	INTERGENIC
SBS	Chr3	34373736	T-G	Hetero	INTERGENIC
SBS	Chr3	37483445	G-T	Hetero	INTERGENIC
SBS	Chr4	3124376	A-G	Homo	INTERGENIC
SBS	Chr4	5669983	G-A	Homo	INTERGENIC
SBS	Chr4	14094394	G-A	Hetero	INTERGENIC
SBS	Chr4	14815159	A-T	Hetero	INTERGENIC
SBS	Chr5	7151201	A-T	Homo	INTERGENIC
SBS	Chr7	29552456	T-A	Hetero	INTRON
SBS	Chr8	11606221	C-T	Hetero	INTERGENIC
SBS	Chr8	17827458	A-G	Homo	INTERGENIC
SBS	Chr9	21735003	A-C	Hetero	INTRON
SBS	Chr11	2542788	T-G	Hetero	INTERGENIC
SBS	Chr11	14413901	C-A	Homo	INTERGENIC
SBS	Chr11	20644444	C-T	Homo	INTERGENIC
SBS	Chr12	13098879	C-T	Homo	INTERGENIC
SBS	Chr12	23906510	C-G	Homo	INTRON
SBS	Chr12	24497362	G-A	Homo	NON_SYNONYMOUS_CODING	OsKitaake12g197600

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr4	5670586	5670587	1
Deletion	Chr12	6593001	6800000	206999	14
Deletion	Chr8	7797980	7797990	10
Deletion	Chr6	9057160	9057166	6
Deletion	Chr10	9848556	9848558	2
Deletion	Chr11	13701211	13701220	9
Deletion	Chr10	13984628	13984699	71
Deletion	Chr9	19998061	19998062	1
Deletion	Chr10	20452763	20452764	1	OsKitaake10g156500
Deletion	Chr8	21906253	21906258	5
Deletion	Chr6	22869946	22869947	1
Deletion	Chr1	23291001	23400000	108999	11
Deletion	Chr8	27690724	27690725	1
Deletion	Chr5	30121645	30121646	1

Variant Type	Chromosome	Position 1	Chromosome	Position 2	Number of Genes
Translocation	Chr12	1303552	Chr1	457927	2
Translocation	Chr12	1304408	Chr1	457920	2

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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