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Mutant Information

Mutant Name	FN1442-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN1442-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) = Low (Between 25% and 74%) For more information, please see this phenotype file

Variant Information

Single base substitutions: 44

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 3306424 G-T Hetero INTERGENIC
SBS Chr1 8831789 A-G Hetero INTERGENIC
SBS Chr1 16127933 G-A Hetero INTERGENIC
SBS Chr1 20150088 G-A Hetero INTERGENIC
SBS Chr1 21396581 C-T Homo INTERGENIC
SBS Chr1 37807526 G-A Homo INTERGENIC
SBS Chr1 39608491 A-T Hetero INTERGENIC
SBS Chr2 15619088 C-A Hetero INTERGENIC
SBS Chr2 21781980 G-A Homo INTERGENIC
SBS Chr3 12109566 C-A Hetero INTERGENIC
SBS Chr3 23100061 C-A Hetero INTERGENIC
SBS Chr3 27837873 C-T Hetero INTERGENIC
SBS Chr4 479099 A-T Hetero INTRON
SBS Chr4 2904598 G-A Homo INTERGENIC
SBS Chr4 3002604 G-T Hetero INTERGENIC
SBS Chr4 3002605 A-T Hetero INTERGENIC
SBS Chr4 5612410 G-A Hetero INTERGENIC
SBS Chr4 9870573 C-T Homo INTERGENIC
SBS Chr4 15211623 G-A Hetero INTERGENIC
SBS Chr4 18561636 T-A Hetero INTRON
SBS Chr4 22473478 G-A Homo NON_SYNONYMOUS_CODING OsKitaake04g132400
SBS Chr5 12350405 G-A Hetero INTERGENIC
SBS Chr5 18972517 C-T Hetero INTERGENIC
SBS Chr6 14243265 T-A Hetero NON_SYNONYMOUS_CODING OsKitaake06g147400
SBS Chr7 4257219 T-A Homo INTERGENIC
SBS Chr7 9843423 G-A Hetero INTERGENIC
SBS Chr7 17345965 T-C Homo INTERGENIC
SBS Chr7 19004504 G-C Hetero INTERGENIC
SBS Chr8 1796473 G-A Homo INTERGENIC
SBS Chr8 4020974 C-A Hetero INTERGENIC
SBS Chr8 8243813 T-C Homo SYNONYMOUS_CODING
SBS Chr8 12493942 A-G Hetero INTERGENIC
SBS Chr9 21383275 G-A Homo INTERGENIC
SBS Chr9 21383295 C-T Homo INTERGENIC
SBS Chr11 5642097 C-T Hetero INTERGENIC
SBS Chr11 13123517 C-A Hetero INTERGENIC
SBS Chr11 21960424 A-T Homo INTRON
SBS Chr11 26822800 A-T Hetero NON_SYNONYMOUS_CODING OsKitaake11g218200
SBS Chr12 969470 G-A Homo NON_SYNONYMOUS_CODING OsKitaake12g014100
SBS Chr12 7778349 C-A Hetero INTERGENIC
SBS Chr12 9533720 G-A Homo INTERGENIC
SBS Chr12 13563978 C-T Homo INTERGENIC
SBS Chr12 25777344 G-T Hetero UTR_3_PRIME
SBS Chr12 26152054 T-G Hetero INTERGENIC

Deletions: 7

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr8 4399181 4399184 3
Deletion Chr5 6380511 6380513 2
Deletion Chr6 6770631 6770635 4
Deletion Chr8 9574715 9574720 5
Deletion Chr9 16351978 16351991 13
Deletion Chr2 22074356 22074360 4
Deletion Chr7 25414824 25414841 17

Insertions: 2

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr1 15190838 15190846 7
Insertion Chr8 9756728 9756730 1

Inversions: 4

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Inversion Chr6 15987351 16178222
Inversion Chr6 15987353 16178228
Inversion Chr9 16814008 16897373
Inversion Chr9 16814012 16897371

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	3306424	G-T	Hetero	INTERGENIC
SBS	Chr1	8831789	A-G	Hetero	INTERGENIC
SBS	Chr1	16127933	G-A	Hetero	INTERGENIC
SBS	Chr1	20150088	G-A	Hetero	INTERGENIC
SBS	Chr1	21396581	C-T	Homo	INTERGENIC
SBS	Chr1	37807526	G-A	Homo	INTERGENIC
SBS	Chr1	39608491	A-T	Hetero	INTERGENIC
SBS	Chr2	15619088	C-A	Hetero	INTERGENIC
SBS	Chr2	21781980	G-A	Homo	INTERGENIC
SBS	Chr3	12109566	C-A	Hetero	INTERGENIC
SBS	Chr3	23100061	C-A	Hetero	INTERGENIC
SBS	Chr3	27837873	C-T	Hetero	INTERGENIC
SBS	Chr4	479099	A-T	Hetero	INTRON
SBS	Chr4	2904598	G-A	Homo	INTERGENIC
SBS	Chr4	3002604	G-T	Hetero	INTERGENIC
SBS	Chr4	3002605	A-T	Hetero	INTERGENIC
SBS	Chr4	5612410	G-A	Hetero	INTERGENIC
SBS	Chr4	9870573	C-T	Homo	INTERGENIC
SBS	Chr4	15211623	G-A	Hetero	INTERGENIC
SBS	Chr4	18561636	T-A	Hetero	INTRON
SBS	Chr4	22473478	G-A	Homo	NON_SYNONYMOUS_CODING	OsKitaake04g132400
SBS	Chr5	12350405	G-A	Hetero	INTERGENIC
SBS	Chr5	18972517	C-T	Hetero	INTERGENIC
SBS	Chr6	14243265	T-A	Hetero	NON_SYNONYMOUS_CODING	OsKitaake06g147400
SBS	Chr7	4257219	T-A	Homo	INTERGENIC
SBS	Chr7	9843423	G-A	Hetero	INTERGENIC
SBS	Chr7	17345965	T-C	Homo	INTERGENIC
SBS	Chr7	19004504	G-C	Hetero	INTERGENIC
SBS	Chr8	1796473	G-A	Homo	INTERGENIC
SBS	Chr8	4020974	C-A	Hetero	INTERGENIC
SBS	Chr8	8243813	T-C	Homo	SYNONYMOUS_CODING
SBS	Chr8	12493942	A-G	Hetero	INTERGENIC
SBS	Chr9	21383275	G-A	Homo	INTERGENIC
SBS	Chr9	21383295	C-T	Homo	INTERGENIC
SBS	Chr11	5642097	C-T	Hetero	INTERGENIC
SBS	Chr11	13123517	C-A	Hetero	INTERGENIC
SBS	Chr11	21960424	A-T	Homo	INTRON
SBS	Chr11	26822800	A-T	Hetero	NON_SYNONYMOUS_CODING	OsKitaake11g218200
SBS	Chr12	969470	G-A	Homo	NON_SYNONYMOUS_CODING	OsKitaake12g014100
SBS	Chr12	7778349	C-A	Hetero	INTERGENIC
SBS	Chr12	9533720	G-A	Homo	INTERGENIC
SBS	Chr12	13563978	C-T	Homo	INTERGENIC
SBS	Chr12	25777344	G-T	Hetero	UTR_3_PRIME
SBS	Chr12	26152054	T-G	Hetero	INTERGENIC

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr8	4399181	4399184	3
Deletion	Chr5	6380511	6380513	2
Deletion	Chr6	6770631	6770635	4
Deletion	Chr8	9574715	9574720	5
Deletion	Chr9	16351978	16351991	13
Deletion	Chr2	22074356	22074360	4
Deletion	Chr7	25414824	25414841	17

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr6	15987351	16178222
Inversion	Chr6	15987353	16178228
Inversion	Chr9	16814008	16897373
Inversion	Chr9	16814012	16897371

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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

Position 2

Number of Genes