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Mutant Information

Mutant Name	FN2596-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN2596-S Alignment File
Seed Availability	Yes [Order Seeds]
Phenotype	TO:0000014 (Panicle Weight) = Very Low (below 24% compare to WT) TO:0000207 (Plant height) = Short (Between 25% and 74%) 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: 67

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 12394765 C-A Hetero INTERGENIC
SBS Chr1 17369028 G-A Hetero NON_SYNONYMOUS_CODING OsKitaake01g178900
SBS Chr1 23517670 T-C Hetero UTR_5_PRIME
SBS Chr1 27256728 C-G Hetero INTRON
SBS Chr1 37531896 T-C Hetero UTR_3_PRIME
SBS Chr1 39972765 G-T Hetero INTERGENIC
SBS Chr1 43535157 C-T Hetero INTERGENIC
SBS Chr2 8044998 T-A Hetero INTERGENIC
SBS Chr2 10113796 C-A Hetero INTERGENIC
SBS Chr2 22133533 C-T Homo INTERGENIC
SBS Chr2 22133535 C-T Homo INTERGENIC
SBS Chr2 26621652 A-G Hetero INTERGENIC
SBS Chr2 27540478 C-G Hetero START_GAINED
SBS Chr2 31340478 G-A Hetero INTERGENIC
SBS Chr3 6280904 C-T Homo INTERGENIC
SBS Chr3 8790507 C-A Hetero INTERGENIC
SBS Chr3 11670421 C-A Hetero INTERGENIC
SBS Chr3 13814024 C-G Hetero NON_SYNONYMOUS_CODING OsKitaake03g182500
SBS Chr3 19225004 C-G Homo INTERGENIC
SBS Chr3 19503309 C-T Hetero INTERGENIC
SBS Chr3 23847782 A-G Hetero INTERGENIC
SBS Chr3 37494522 C-A Hetero SYNONYMOUS_CODING
SBS Chr4 8201881 A-C Homo INTERGENIC
SBS Chr4 13802206 C-T Hetero INTERGENIC
SBS Chr4 24749310 C-T Homo INTRON
SBS Chr4 24749311 C-T Homo INTRON
SBS Chr4 28500934 C-T Homo START_GAINED
SBS Chr5 1366102 C-G Homo INTERGENIC
SBS Chr5 3098807 C-A Hetero INTERGENIC
SBS Chr5 5168179 G-A Hetero INTERGENIC
SBS Chr6 2608741 T-G Hetero INTERGENIC
SBS Chr6 2762128 A-G Homo INTERGENIC
SBS Chr6 3689257 G-A Hetero INTERGENIC
SBS Chr6 13220274 A-T Hetero NON_SYNONYMOUS_CODING OsKitaake06g139500
SBS Chr6 14578329 G-A Hetero INTRON
SBS Chr6 17366104 C-T Hetero INTERGENIC
SBS Chr6 22371031 G-A Hetero INTERGENIC
SBS Chr6 29287431 C-G Hetero INTERGENIC
SBS Chr7 2870230 T-C Hetero INTERGENIC
SBS Chr7 6124783 T-A Hetero INTERGENIC
SBS Chr7 7097339 C-T Hetero INTERGENIC
SBS Chr7 7174965 C-T Hetero INTERGENIC
SBS Chr7 27548583 C-T Hetero INTERGENIC
SBS Chr8 11303626 G-A Homo INTERGENIC
SBS Chr8 12742579 T-C Hetero INTERGENIC
SBS Chr8 14719574 G-A Homo INTERGENIC
SBS Chr8 21436857 C-G Homo INTERGENIC
SBS Chr8 22795535 A-T Hetero INTERGENIC
SBS Chr8 24258260 C-T Hetero INTERGENIC
SBS Chr9 2143714 G-T Hetero INTERGENIC
SBS Chr9 4118685 C-T Homo INTERGENIC
SBS Chr9 4379991 G-A Hetero INTERGENIC
SBS Chr9 5525225 C-T Hetero INTERGENIC
SBS Chr9 6693836 G-A Hetero INTERGENIC
SBS Chr9 11893071 G-A Hetero INTERGENIC
SBS Chr9 16746930 G-A Hetero INTERGENIC
SBS Chr9 19480683 T-C Homo INTERGENIC
SBS Chr9 22690450 C-T Homo INTERGENIC
SBS Chr10 1336538 T-C Hetero INTERGENIC
SBS Chr10 11768045 C-T Hetero INTERGENIC
SBS Chr11 12275032 T-G Homo INTRON
SBS Chr11 12422881 T-A Hetero INTERGENIC
SBS Chr11 13335606 A-G Homo INTERGENIC
SBS Chr11 22997972 T-A Hetero INTRON
SBS Chr12 2142631 C-T Homo INTERGENIC
SBS Chr12 5829793 C-T Hetero INTERGENIC
SBS Chr12 9313504 C-T Hetero INTRON

Deletions: 8

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr3 1943947 1943956 9
Deletion Chr4 5743008 5743010 2
Deletion Chr5 15050011 15050012 1
Deletion Chr6 24273302 24273304 2
Deletion Chr6 24831068 24831069 1
Deletion Chr1 25004844 25004851 7
Deletion Chr3 25288704 25288725 21 OsKitaake03g267300
Deletion Chr1 29861268 29861278 10

Insertions: 2

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr7 3185965 3185968 2
Insertion Chr7 8785773 8785776 2

Translocations: 2

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes

Translocation Chr12 19535976 Chr9 7875452 2
Translocation Chr12 19535977 Chr9 7874998 2

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	12394765	C-A	Hetero	INTERGENIC
SBS	Chr1	17369028	G-A	Hetero	NON_SYNONYMOUS_CODING	OsKitaake01g178900
SBS	Chr1	23517670	T-C	Hetero	UTR_5_PRIME
SBS	Chr1	27256728	C-G	Hetero	INTRON
SBS	Chr1	37531896	T-C	Hetero	UTR_3_PRIME
SBS	Chr1	39972765	G-T	Hetero	INTERGENIC
SBS	Chr1	43535157	C-T	Hetero	INTERGENIC
SBS	Chr2	8044998	T-A	Hetero	INTERGENIC
SBS	Chr2	10113796	C-A	Hetero	INTERGENIC
SBS	Chr2	22133533	C-T	Homo	INTERGENIC
SBS	Chr2	22133535	C-T	Homo	INTERGENIC
SBS	Chr2	26621652	A-G	Hetero	INTERGENIC
SBS	Chr2	27540478	C-G	Hetero	START_GAINED
SBS	Chr2	31340478	G-A	Hetero	INTERGENIC
SBS	Chr3	6280904	C-T	Homo	INTERGENIC
SBS	Chr3	8790507	C-A	Hetero	INTERGENIC
SBS	Chr3	11670421	C-A	Hetero	INTERGENIC
SBS	Chr3	13814024	C-G	Hetero	NON_SYNONYMOUS_CODING	OsKitaake03g182500
SBS	Chr3	19225004	C-G	Homo	INTERGENIC
SBS	Chr3	19503309	C-T	Hetero	INTERGENIC
SBS	Chr3	23847782	A-G	Hetero	INTERGENIC
SBS	Chr3	37494522	C-A	Hetero	SYNONYMOUS_CODING
SBS	Chr4	8201881	A-C	Homo	INTERGENIC
SBS	Chr4	13802206	C-T	Hetero	INTERGENIC
SBS	Chr4	24749310	C-T	Homo	INTRON
SBS	Chr4	24749311	C-T	Homo	INTRON
SBS	Chr4	28500934	C-T	Homo	START_GAINED
SBS	Chr5	1366102	C-G	Homo	INTERGENIC
SBS	Chr5	3098807	C-A	Hetero	INTERGENIC
SBS	Chr5	5168179	G-A	Hetero	INTERGENIC
SBS	Chr6	2608741	T-G	Hetero	INTERGENIC
SBS	Chr6	2762128	A-G	Homo	INTERGENIC
SBS	Chr6	3689257	G-A	Hetero	INTERGENIC
SBS	Chr6	13220274	A-T	Hetero	NON_SYNONYMOUS_CODING	OsKitaake06g139500
SBS	Chr6	14578329	G-A	Hetero	INTRON
SBS	Chr6	17366104	C-T	Hetero	INTERGENIC
SBS	Chr6	22371031	G-A	Hetero	INTERGENIC
SBS	Chr6	29287431	C-G	Hetero	INTERGENIC
SBS	Chr7	2870230	T-C	Hetero	INTERGENIC
SBS	Chr7	6124783	T-A	Hetero	INTERGENIC
SBS	Chr7	7097339	C-T	Hetero	INTERGENIC
SBS	Chr7	7174965	C-T	Hetero	INTERGENIC
SBS	Chr7	27548583	C-T	Hetero	INTERGENIC
SBS	Chr8	11303626	G-A	Homo	INTERGENIC
SBS	Chr8	12742579	T-C	Hetero	INTERGENIC
SBS	Chr8	14719574	G-A	Homo	INTERGENIC
SBS	Chr8	21436857	C-G	Homo	INTERGENIC
SBS	Chr8	22795535	A-T	Hetero	INTERGENIC
SBS	Chr8	24258260	C-T	Hetero	INTERGENIC
SBS	Chr9	2143714	G-T	Hetero	INTERGENIC
SBS	Chr9	4118685	C-T	Homo	INTERGENIC
SBS	Chr9	4379991	G-A	Hetero	INTERGENIC
SBS	Chr9	5525225	C-T	Hetero	INTERGENIC
SBS	Chr9	6693836	G-A	Hetero	INTERGENIC
SBS	Chr9	11893071	G-A	Hetero	INTERGENIC
SBS	Chr9	16746930	G-A	Hetero	INTERGENIC
SBS	Chr9	19480683	T-C	Homo	INTERGENIC
SBS	Chr9	22690450	C-T	Homo	INTERGENIC
SBS	Chr10	1336538	T-C	Hetero	INTERGENIC
SBS	Chr10	11768045	C-T	Hetero	INTERGENIC
SBS	Chr11	12275032	T-G	Homo	INTRON
SBS	Chr11	12422881	T-A	Hetero	INTERGENIC
SBS	Chr11	13335606	A-G	Homo	INTERGENIC
SBS	Chr11	22997972	T-A	Hetero	INTRON
SBS	Chr12	2142631	C-T	Homo	INTERGENIC
SBS	Chr12	5829793	C-T	Hetero	INTERGENIC
SBS	Chr12	9313504	C-T	Hetero	INTRON

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr3	1943947	1943956	9
Deletion	Chr4	5743008	5743010	2
Deletion	Chr5	15050011	15050012	1
Deletion	Chr6	24273302	24273304	2
Deletion	Chr6	24831068	24831069	1
Deletion	Chr1	25004844	25004851	7
Deletion	Chr3	25288704	25288725	21	OsKitaake03g267300
Deletion	Chr1	29861268	29861278	10

Variant Type	Chromosome	Position 1	Chromosome	Position 2	Number of Genes
Translocation	Chr12	19535976	Chr9	7875452	2
Translocation	Chr12	19535977	Chr9	7874998	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