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Mutant Information

Mutant Name	FN2540-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN2540-S Alignment File
Seed Availability	Yes [Order Seeds]
Phenotype	TO:0000430 (Germination Rate) = Normal (Between 75% and 125%) For more information, please see this phenotype file

Variant Information

Single base substitutions: 49

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 2298064 A-G Hetero INTERGENIC
SBS Chr1 2999860 A-G Homo INTERGENIC
SBS Chr1 6545964 G-A Homo INTERGENIC
SBS Chr1 12194254 C-T Hetero INTERGENIC
SBS Chr2 3465468 A-G Hetero INTERGENIC
SBS Chr2 5546355 G-A Hetero INTERGENIC
SBS Chr2 6530464 C-T Hetero NON_SYNONYMOUS_CODING OsKitaake02g088800
SBS Chr2 7220934 G-T Hetero INTERGENIC
SBS Chr3 6273382 T-C Hetero INTERGENIC
SBS Chr3 8975425 C-T Hetero INTERGENIC
SBS Chr3 19520055 G-T Homo INTERGENIC
SBS Chr3 32263958 T-A Hetero NON_SYNONYMOUS_CODING OsKitaake03g342301
SBS Chr4 2532399 C-A Hetero INTERGENIC
SBS Chr4 13463598 T-C Hetero INTERGENIC
SBS Chr4 16206090 G-T Hetero INTERGENIC
SBS Chr4 16243542 A-T Hetero NON_SYNONYMOUS_CODING OsKitaake04g079700
SBS Chr4 16617800 G-T Hetero INTERGENIC
SBS Chr4 18121307 C-T Homo INTERGENIC
SBS Chr4 18942781 A-G Hetero INTRON
SBS Chr4 34149371 G-A Hetero INTERGENIC
SBS Chr4 34149372 G-T Hetero INTERGENIC
SBS Chr5 3484976 G-T Hetero NON_SYNONYMOUS_CODING OsKitaake05g042000
SBS Chr5 9751586 T-A Hetero INTERGENIC
SBS Chr5 14830026 G-A Hetero INTERGENIC
SBS Chr6 1719869 C-A Homo INTERGENIC
SBS Chr6 8336297 T-C Hetero INTERGENIC
SBS Chr6 10027516 T-A Hetero INTERGENIC
SBS Chr6 14109567 T-C Hetero INTERGENIC
SBS Chr6 14109568 T-A Hetero INTERGENIC
SBS Chr7 8476191 A-G Hetero SYNONYMOUS_CODING
SBS Chr7 9795062 A-T Hetero INTERGENIC
SBS Chr7 10386081 G-A Hetero INTERGENIC
SBS Chr7 13400400 C-A Hetero INTERGENIC
SBS Chr8 24112961 C-T Hetero NON_SYNONYMOUS_CODING OsKitaake08g186200
SBS Chr9 9827576 A-C Homo INTERGENIC
SBS Chr9 20018086 C-T Hetero INTERGENIC
SBS Chr10 1745909 A-G Homo NON_SYNONYMOUS_CODING OsKitaake10g012500
SBS Chr10 6505106 C-T Homo INTERGENIC
SBS Chr10 17252891 T-A Hetero INTERGENIC
SBS Chr10 23310410 C-T Hetero INTERGENIC
SBS Chr11 2987019 C-T Homo UTR_5_PRIME
SBS Chr11 5397831 T-G Hetero INTERGENIC
SBS Chr11 6381066 C-T Homo INTERGENIC
SBS Chr11 24364916 G-A Hetero INTERGENIC
SBS Chr11 27664412 G-A Hetero NON_SYNONYMOUS_CODING OsKitaake11g225400
SBS Chr12 1179423 G-C Hetero INTERGENIC
SBS Chr12 12272200 T-G Hetero INTERGENIC
SBS Chr12 24158851 C-T Hetero INTERGENIC
SBS Chr12 24471889 G-T Hetero INTERGENIC

Deletions: 14

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr6 4587601 4587604 3
Deletion Chr12 5352418 5352426 8
Deletion Chr5 7901531 7901546 15
Deletion Chr5 8178072 8178099 27
Deletion Chr4 8292258 8292260 2
Deletion Chr6 9029505 9029511 6
Deletion Chr8 9432809 9432812 3
Deletion Chr5 13155346 13155350 4
Deletion Chr3 13576276 13576298 22
Deletion Chr1 16847027 16847028 1
Deletion Chr7 18850165 18850167 2
Deletion Chr6 19042508 19042518 10
Deletion Chr3 22269348 22269375 27
Deletion Chr1 25670436 25670451 15

Insertions: 4

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr3 12957254 12957257 2
Insertion Chr8 18171081 18171084 2
Insertion Chr9 14732528 14732531 2
Insertion Chr4 18297099 18297101 1

Translocations: 4

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes

Translocation Chr3 165080 Chr1 5638973 OsKitaake03g002600
Translocation Chr3 165666 Chr1 5639012 OsKitaake03g002600
Translocation Chr8 1557598 Chr4 7552332 OsKitaake08g019300
Translocation Chr8 1557599 Chr4 7553284 OsKitaake08g019300

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	2298064	A-G	Hetero	INTERGENIC
SBS	Chr1	2999860	A-G	Homo	INTERGENIC
SBS	Chr1	6545964	G-A	Homo	INTERGENIC
SBS	Chr1	12194254	C-T	Hetero	INTERGENIC
SBS	Chr2	3465468	A-G	Hetero	INTERGENIC
SBS	Chr2	5546355	G-A	Hetero	INTERGENIC
SBS	Chr2	6530464	C-T	Hetero	NON_SYNONYMOUS_CODING	OsKitaake02g088800
SBS	Chr2	7220934	G-T	Hetero	INTERGENIC
SBS	Chr3	6273382	T-C	Hetero	INTERGENIC
SBS	Chr3	8975425	C-T	Hetero	INTERGENIC
SBS	Chr3	19520055	G-T	Homo	INTERGENIC
SBS	Chr3	32263958	T-A	Hetero	NON_SYNONYMOUS_CODING	OsKitaake03g342301
SBS	Chr4	2532399	C-A	Hetero	INTERGENIC
SBS	Chr4	13463598	T-C	Hetero	INTERGENIC
SBS	Chr4	16206090	G-T	Hetero	INTERGENIC
SBS	Chr4	16243542	A-T	Hetero	NON_SYNONYMOUS_CODING	OsKitaake04g079700
SBS	Chr4	16617800	G-T	Hetero	INTERGENIC
SBS	Chr4	18121307	C-T	Homo	INTERGENIC
SBS	Chr4	18942781	A-G	Hetero	INTRON
SBS	Chr4	34149371	G-A	Hetero	INTERGENIC
SBS	Chr4	34149372	G-T	Hetero	INTERGENIC
SBS	Chr5	3484976	G-T	Hetero	NON_SYNONYMOUS_CODING	OsKitaake05g042000
SBS	Chr5	9751586	T-A	Hetero	INTERGENIC
SBS	Chr5	14830026	G-A	Hetero	INTERGENIC
SBS	Chr6	1719869	C-A	Homo	INTERGENIC
SBS	Chr6	8336297	T-C	Hetero	INTERGENIC
SBS	Chr6	10027516	T-A	Hetero	INTERGENIC
SBS	Chr6	14109567	T-C	Hetero	INTERGENIC
SBS	Chr6	14109568	T-A	Hetero	INTERGENIC
SBS	Chr7	8476191	A-G	Hetero	SYNONYMOUS_CODING
SBS	Chr7	9795062	A-T	Hetero	INTERGENIC
SBS	Chr7	10386081	G-A	Hetero	INTERGENIC
SBS	Chr7	13400400	C-A	Hetero	INTERGENIC
SBS	Chr8	24112961	C-T	Hetero	NON_SYNONYMOUS_CODING	OsKitaake08g186200
SBS	Chr9	9827576	A-C	Homo	INTERGENIC
SBS	Chr9	20018086	C-T	Hetero	INTERGENIC
SBS	Chr10	1745909	A-G	Homo	NON_SYNONYMOUS_CODING	OsKitaake10g012500
SBS	Chr10	6505106	C-T	Homo	INTERGENIC
SBS	Chr10	17252891	T-A	Hetero	INTERGENIC
SBS	Chr10	23310410	C-T	Hetero	INTERGENIC
SBS	Chr11	2987019	C-T	Homo	UTR_5_PRIME
SBS	Chr11	5397831	T-G	Hetero	INTERGENIC
SBS	Chr11	6381066	C-T	Homo	INTERGENIC
SBS	Chr11	24364916	G-A	Hetero	INTERGENIC
SBS	Chr11	27664412	G-A	Hetero	NON_SYNONYMOUS_CODING	OsKitaake11g225400
SBS	Chr12	1179423	G-C	Hetero	INTERGENIC
SBS	Chr12	12272200	T-G	Hetero	INTERGENIC
SBS	Chr12	24158851	C-T	Hetero	INTERGENIC
SBS	Chr12	24471889	G-T	Hetero	INTERGENIC

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr6	4587601	4587604	3
Deletion	Chr12	5352418	5352426	8
Deletion	Chr5	7901531	7901546	15
Deletion	Chr5	8178072	8178099	27
Deletion	Chr4	8292258	8292260	2
Deletion	Chr6	9029505	9029511	6
Deletion	Chr8	9432809	9432812	3
Deletion	Chr5	13155346	13155350	4
Deletion	Chr3	13576276	13576298	22
Deletion	Chr1	16847027	16847028	1
Deletion	Chr7	18850165	18850167	2
Deletion	Chr6	19042508	19042518	10
Deletion	Chr3	22269348	22269375	27
Deletion	Chr1	25670436	25670451	15

Variant Type	Chromosome	Position 1	Chromosome	Position 2	Number of Genes
Translocation	Chr3	165080	Chr1	5638973	OsKitaake03g002600
Translocation	Chr3	165666	Chr1	5639012	OsKitaake03g002600
Translocation	Chr8	1557598	Chr4	7552332	OsKitaake08g019300
Translocation	Chr8	1557599	Chr4	7553284	OsKitaake08g019300

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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