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Mutant Information

Mutant Name	FN1463-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN1463-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) = Normal (Between 75% and 125%) TO:0000430 (Germination Rate) = Normal (Between 75% and 125%) For more information, please see this phenotype file

Variant Information

Single base substitutions: 35

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 334009 A-G Hetero UTR_5_PRIME
SBS Chr1 1870712 C-A Homo INTRON
SBS Chr1 2200874 T-C Homo INTERGENIC
SBS Chr1 31683221 A-G Hetero INTERGENIC
SBS Chr1 40986141 T-C Hetero INTERGENIC
SBS Chr2 10031086 C-G Homo UTR_3_PRIME
SBS Chr3 4103744 G-A Homo INTERGENIC
SBS Chr3 10330335 T-A Homo INTERGENIC
SBS Chr3 34429636 C-A Homo INTERGENIC
SBS Chr4 6446231 A-G Homo INTERGENIC
SBS Chr4 8528062 T-A Homo INTERGENIC
SBS Chr4 15755859 G-A Hetero INTERGENIC
SBS Chr4 23926204 C-T Hetero INTERGENIC
SBS Chr5 6849696 T-A Homo INTERGENIC
SBS Chr5 11074234 C-T Homo INTERGENIC
SBS Chr6 3897807 A-G Hetero INTRON
SBS Chr6 12571044 G-T Homo NON_SYNONYMOUS_CODING OsKitaake06g134200
SBS Chr7 5935879 A-T Hetero INTERGENIC
SBS Chr7 7691927 T-G Hetero INTERGENIC
SBS Chr7 9704021 T-A Hetero INTERGENIC
SBS Chr7 18864556 A-T Homo INTERGENIC
SBS Chr8 12877504 G-A Hetero INTERGENIC
SBS Chr8 13298119 G-C Hetero SYNONYMOUS_CODING
SBS Chr8 22541746 G-A Homo INTERGENIC
SBS Chr9 1029430 T-G Hetero INTERGENIC
SBS Chr9 8886082 C-T Hetero INTERGENIC
SBS Chr9 17209900 C-T Hetero UTR_3_PRIME
SBS Chr10 1892250 G-A Hetero INTERGENIC
SBS Chr10 1892251 C-A Hetero INTERGENIC
SBS Chr10 11113386 C-T Hetero INTERGENIC
SBS Chr11 22673405 C-T Homo INTERGENIC
SBS Chr12 4404450 A-T Hetero INTERGENIC
SBS Chr12 7454153 C-A Hetero INTERGENIC
SBS Chr12 9736637 C-T Homo INTERGENIC
SBS Chr12 25688912 A-G Hetero INTRON

Deletions: 51

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr3 1082001 1104000 21999 OsKitaake03g016901
Deletion Chr5 1096001 1108000 11999 2
Deletion Chr7 1485564 1485567 3
Deletion Chr9 1600001 1618000 17999 OsKitaake09g009200
Deletion Chr12 1739001 1748000 8999 OsKitaake12g026400
Deletion Chr4 2449001 2467000 17999
Deletion Chr10 3487001 3518000 30999 OsKitaake10g026400
Deletion Chr9 3717001 3732000 14999
Deletion Chr9 3928001 3948000 19999 2
Deletion Chr11 4486001 4532000 45999 4
Deletion Chr2 5231001 5243000 11999 2
Deletion Chr2 5809001 5817000 7999 OsKitaake02g080100
Deletion Chr7 7548001 7557000 8999
Deletion Chr2 8449752 8449755 3
Deletion Chr9 8713137 8713140 3
Deletion Chr9 8756001 8779000 22999 OsKitaake09g051400
Deletion Chr5 9021219 9021229 10
Deletion Chr11 9467001 9484000 16999 2
Deletion Chr6 9916001 9932000 15999 OsKitaake06g115100
Deletion Chr11 10793926 10793928 2
Deletion Chr12 10835001 10852000 16999 3
Deletion Chr12 11657384 11657385 1
Deletion Chr9 12285234 12285235 1
Deletion Chr4 14095253 14095254 1
Deletion Chr12 14452458 14452462 4
Deletion Chr6 14461001 14470000 8999 OsKitaake06g148200
Deletion Chr6 14653001 14730000 76999 2
Deletion Chr1 14674001 14695000 20999 OsKitaake01g166200
Deletion Chr2 15108001 15151000 42999 3
Deletion Chr10 16120001 16486000 365999 43
Deletion Chr10 16494001 16631000 136999 19
Deletion Chr5 16869001 16875000 5999 OsKitaake05g128800
Deletion Chr6 16972001 16983000 10999 OsKitaake06g159500
Deletion Chr2 17547001 17560000 12999 OsKitaake02g176100
Deletion Chr4 18247001 18256000 8999 2
Deletion Chr4 19337001 19358000 20999
Deletion Chr9 20018999 20019010 11
Deletion Chr7 20322901 20322904 3
Deletion Chr12 20633950 20633955 5
Deletion Chr12 22038302 22038307 5 OsKitaake12g173300
Deletion Chr8 23771442 23771462 20
Deletion Chr3 23841150 23841159 9
Deletion Chr3 25108001 25132000 23999 3
Deletion Chr12 25777119 25777130 11
Deletion Chr11 26579001 26594000 14999 3
Deletion Chr3 28650001 28668000 17999
Deletion Chr3 29235961 29235965 4 OsKitaake03g304100
Deletion Chr2 29670107 29670110 3
Deletion Chr2 34131001 34142000 10999 OsKitaake02g354400
Deletion Chr1 35778001 35788000 9999 3
Deletion Chr1 42304001 42322000 17999 OsKitaake01g466400

Insertions: 3

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr2 28404876 28404879 2
Insertion Chr11 11259765 11259768 2 OsKitaake11g107900
Insertion Chr12 11693872 11693874 1

Inversions: 7

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Inversion Chr6 3947875 3997796 2
Inversion Chr6 3947878 3997811 2
Inversion Chr6 13428912 13661365 OsKitaake06g142900
Inversion Chr6 13428933 13661382 OsKitaake06g142900
Inversion Chr6 14470406 14726648
Inversion Chr1 41950637 42224391 OsKitaake01g459700
Inversion Chr1 41950657 42224416 OsKitaake01g459700

Translocations: 3

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes

Translocation Chr8 362629 Chr2 556500 OsKitaake08g005300
Translocation Chr8 362632 Chr2 557537 OsKitaake08g005300
Translocation Chr3 4875418 Chr1 29867692 OsKitaake03g070200

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	334009	A-G	Hetero	UTR_5_PRIME
SBS	Chr1	1870712	C-A	Homo	INTRON
SBS	Chr1	2200874	T-C	Homo	INTERGENIC
SBS	Chr1	31683221	A-G	Hetero	INTERGENIC
SBS	Chr1	40986141	T-C	Hetero	INTERGENIC
SBS	Chr2	10031086	C-G	Homo	UTR_3_PRIME
SBS	Chr3	4103744	G-A	Homo	INTERGENIC
SBS	Chr3	10330335	T-A	Homo	INTERGENIC
SBS	Chr3	34429636	C-A	Homo	INTERGENIC
SBS	Chr4	6446231	A-G	Homo	INTERGENIC
SBS	Chr4	8528062	T-A	Homo	INTERGENIC
SBS	Chr4	15755859	G-A	Hetero	INTERGENIC
SBS	Chr4	23926204	C-T	Hetero	INTERGENIC
SBS	Chr5	6849696	T-A	Homo	INTERGENIC
SBS	Chr5	11074234	C-T	Homo	INTERGENIC
SBS	Chr6	3897807	A-G	Hetero	INTRON
SBS	Chr6	12571044	G-T	Homo	NON_SYNONYMOUS_CODING	OsKitaake06g134200
SBS	Chr7	5935879	A-T	Hetero	INTERGENIC
SBS	Chr7	7691927	T-G	Hetero	INTERGENIC
SBS	Chr7	9704021	T-A	Hetero	INTERGENIC
SBS	Chr7	18864556	A-T	Homo	INTERGENIC
SBS	Chr8	12877504	G-A	Hetero	INTERGENIC
SBS	Chr8	13298119	G-C	Hetero	SYNONYMOUS_CODING
SBS	Chr8	22541746	G-A	Homo	INTERGENIC
SBS	Chr9	1029430	T-G	Hetero	INTERGENIC
SBS	Chr9	8886082	C-T	Hetero	INTERGENIC
SBS	Chr9	17209900	C-T	Hetero	UTR_3_PRIME
SBS	Chr10	1892250	G-A	Hetero	INTERGENIC
SBS	Chr10	1892251	C-A	Hetero	INTERGENIC
SBS	Chr10	11113386	C-T	Hetero	INTERGENIC
SBS	Chr11	22673405	C-T	Homo	INTERGENIC
SBS	Chr12	4404450	A-T	Hetero	INTERGENIC
SBS	Chr12	7454153	C-A	Hetero	INTERGENIC
SBS	Chr12	9736637	C-T	Homo	INTERGENIC
SBS	Chr12	25688912	A-G	Hetero	INTRON

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr3	1082001	1104000	21999	OsKitaake03g016901
Deletion	Chr5	1096001	1108000	11999	2
Deletion	Chr7	1485564	1485567	3
Deletion	Chr9	1600001	1618000	17999	OsKitaake09g009200
Deletion	Chr12	1739001	1748000	8999	OsKitaake12g026400
Deletion	Chr4	2449001	2467000	17999
Deletion	Chr10	3487001	3518000	30999	OsKitaake10g026400
Deletion	Chr9	3717001	3732000	14999
Deletion	Chr9	3928001	3948000	19999	2
Deletion	Chr11	4486001	4532000	45999	4
Deletion	Chr2	5231001	5243000	11999	2
Deletion	Chr2	5809001	5817000	7999	OsKitaake02g080100
Deletion	Chr7	7548001	7557000	8999
Deletion	Chr2	8449752	8449755	3
Deletion	Chr9	8713137	8713140	3
Deletion	Chr9	8756001	8779000	22999	OsKitaake09g051400
Deletion	Chr5	9021219	9021229	10
Deletion	Chr11	9467001	9484000	16999	2
Deletion	Chr6	9916001	9932000	15999	OsKitaake06g115100
Deletion	Chr11	10793926	10793928	2
Deletion	Chr12	10835001	10852000	16999	3
Deletion	Chr12	11657384	11657385	1
Deletion	Chr9	12285234	12285235	1
Deletion	Chr4	14095253	14095254	1
Deletion	Chr12	14452458	14452462	4
Deletion	Chr6	14461001	14470000	8999	OsKitaake06g148200
Deletion	Chr6	14653001	14730000	76999	2
Deletion	Chr1	14674001	14695000	20999	OsKitaake01g166200
Deletion	Chr2	15108001	15151000	42999	3
Deletion	Chr10	16120001	16486000	365999	43
Deletion	Chr10	16494001	16631000	136999	19
Deletion	Chr5	16869001	16875000	5999	OsKitaake05g128800
Deletion	Chr6	16972001	16983000	10999	OsKitaake06g159500
Deletion	Chr2	17547001	17560000	12999	OsKitaake02g176100
Deletion	Chr4	18247001	18256000	8999	2
Deletion	Chr4	19337001	19358000	20999
Deletion	Chr9	20018999	20019010	11
Deletion	Chr7	20322901	20322904	3
Deletion	Chr12	20633950	20633955	5
Deletion	Chr12	22038302	22038307	5	OsKitaake12g173300
Deletion	Chr8	23771442	23771462	20
Deletion	Chr3	23841150	23841159	9
Deletion	Chr3	25108001	25132000	23999	3
Deletion	Chr12	25777119	25777130	11
Deletion	Chr11	26579001	26594000	14999	3
Deletion	Chr3	28650001	28668000	17999
Deletion	Chr3	29235961	29235965	4	OsKitaake03g304100
Deletion	Chr2	29670107	29670110	3
Deletion	Chr2	34131001	34142000	10999	OsKitaake02g354400
Deletion	Chr1	35778001	35788000	9999	3
Deletion	Chr1	42304001	42322000	17999	OsKitaake01g466400

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr6	3947875	3997796	2
Inversion	Chr6	3947878	3997811	2
Inversion	Chr6	13428912	13661365	OsKitaake06g142900
Inversion	Chr6	13428933	13661382	OsKitaake06g142900
Inversion	Chr6	14470406	14726648
Inversion	Chr1	41950637	42224391	OsKitaake01g459700
Inversion	Chr1	41950657	42224416	OsKitaake01g459700

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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

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes