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Mutant Information

Mutant Name	FN1561-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN1561-S Alignment File
Seed Availability	Yes [Order Seeds]
Phenotype	TO:0000326 (Leaf Color) = Normal 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: 55

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 8954143 T-C Hetero INTERGENIC
SBS Chr1 10717446 C-T Hetero INTERGENIC
SBS Chr1 13934287 G-T Hetero INTERGENIC
SBS Chr1 15555590 A-T Hetero INTERGENIC
SBS Chr1 15988070 G-A Hetero INTERGENIC
SBS Chr1 20005503 A-T Hetero INTRON
SBS Chr1 24935853 C-T Homo INTERGENIC
SBS Chr1 40707606 G-A Hetero INTRON
SBS Chr2 30626549 T-A Hetero INTERGENIC
SBS Chr3 4638757 G-A Hetero INTERGENIC
SBS Chr3 21340057 C-T Homo INTERGENIC
SBS Chr3 23916477 C-T Homo INTERGENIC
SBS Chr3 31305442 C-T Homo INTRON
SBS Chr4 3291344 C-T Hetero INTERGENIC
SBS Chr4 11317275 C-A Hetero INTERGENIC
SBS Chr4 17760283 A-G Hetero INTERGENIC
SBS Chr4 21359279 G-A Hetero INTERGENIC
SBS Chr5 5883624 A-G Hetero INTERGENIC
SBS Chr5 12814724 G-A Hetero INTERGENIC
SBS Chr5 14218497 G-T Hetero INTERGENIC
SBS Chr5 17561498 G-A Hetero NON_SYNONYMOUS_CODING OsKitaake05g134600
SBS Chr5 27501906 T-G Hetero INTERGENIC
SBS Chr5 28210889 G-A Homo NON_SYNONYMOUS_CODING OsKitaake05g261400
SBS Chr6 4883706 T-A Hetero INTERGENIC
SBS Chr6 18387645 G-T Hetero INTERGENIC
SBS Chr6 23883013 C-T Hetero INTERGENIC
SBS Chr7 12158364 C-T Homo INTERGENIC
SBS Chr8 9863145 G-A Hetero NON_SYNONYMOUS_CODING OsKitaake08g091700
SBS Chr8 14020210 G-A Hetero INTRON
SBS Chr8 14843572 G-A Hetero INTERGENIC
SBS Chr8 25667308 A-T Homo INTERGENIC
SBS Chr8 26561489 A-T Hetero INTRON
SBS Chr8 28421811 G-A Hetero INTERGENIC
SBS Chr9 656573 C-T Hetero INTERGENIC
SBS Chr9 3907507 C-T Homo INTERGENIC
SBS Chr9 5139512 T-C Hetero INTERGENIC
SBS Chr9 9755512 C-A Hetero INTRON
SBS Chr9 19437079 G-T Hetero SYNONYMOUS_CODING
SBS Chr9 19437080 G-T Hetero NON_SYNONYMOUS_CODING OsKitaake09g158200
SBS Chr9 22227353 G-A Hetero INTRON
SBS Chr10 9880467 G-A Hetero INTRON
SBS Chr10 11717773 A-C Hetero INTERGENIC
SBS Chr10 15683704 A-T Hetero INTERGENIC
SBS Chr11 11165539 C-A Hetero INTERGENIC
SBS Chr11 14118919 G-A Hetero INTERGENIC
SBS Chr11 15374394 C-A Hetero INTERGENIC
SBS Chr11 17047646 A-G Hetero UTR_5_PRIME
SBS Chr11 20466539 C-G Hetero INTRON
SBS Chr11 26235508 G-A Hetero INTERGENIC
SBS Chr12 5713474 T-G Hetero INTERGENIC
SBS Chr12 6520054 G-A Hetero INTERGENIC
SBS Chr12 7553514 T-C Hetero INTRON
SBS Chr12 18434290 A-T Homo INTERGENIC
SBS Chr12 18434291 G-T Homo INTERGENIC
SBS Chr12 25940761 A-T Homo INTERGENIC

Deletions: 24

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr4 4760001 4953000 192999 4
Deletion Chr8 5255001 5272000 16999 OsKitaake08g057000
Deletion Chr7 5265280 5265281 1
Deletion Chr8 10097126 10097128 2
Deletion Chr9 10386447 10386448 1
Deletion Chr4 10479001 10493000 13999
Deletion Chr9 10996001 11046000 49999 6
Deletion Chr7 11282046 11282048 2
Deletion Chr7 12024001 12052000 27999
Deletion Chr12 12588001 12617000 28999 5
Deletion Chr1 17189332 17189497 165
Deletion Chr1 17242104 17242106 2
Deletion Chr12 18532428 18532431 3
Deletion Chr7 19175786 19175789 3
Deletion Chr12 19303969 19303980 11
Deletion Chr5 21335001 21352000 16999 OsKitaake05g172900
Deletion Chr1 21788083 21788089 6
Deletion Chr7 22294867 22294874 7 OsKitaake07g188500
Deletion Chr3 24761686 24761693 7
Deletion Chr12 26732242 26732245 3
Deletion Chr4 27590516 27590520 4
Deletion Chr6 27684001 27703000 18999 OsKitaake06g250900
Deletion Chr5 30223346 30223347 1
Deletion Chr1 41343001 41361000 17999

Insertions: 5

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr5 14569030 14569033 2
Insertion Chr6 7890827 7890830 2
Insertion Chr8 17457026 17457028 1
Insertion Chr2 27446171 27446176 4 OsKitaake02g275800
Insertion Chr10 5415995 5415997 1

Inversions: 6

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Inversion Chr11 8735266 8754055 OsKitaake11g094400
Inversion Chr11 8754058 8791357
Inversion Chr8 15276841 15506118 OsKitaake08g119200
Inversion Chr8 15506106 15578855
Inversion Chr1 41416022 41791232 OsKitaake01g457100
Inversion Chr1 41416032 41791244 OsKitaake01g457100

Translocations: 2

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes

Translocation Chr11 8735270 Chr4 35823170 OsKitaake11g094400
Translocation Chr11 8736160 Chr4 35823930 OsKitaake11g094400

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	8954143	T-C	Hetero	INTERGENIC
SBS	Chr1	10717446	C-T	Hetero	INTERGENIC
SBS	Chr1	13934287	G-T	Hetero	INTERGENIC
SBS	Chr1	15555590	A-T	Hetero	INTERGENIC
SBS	Chr1	15988070	G-A	Hetero	INTERGENIC
SBS	Chr1	20005503	A-T	Hetero	INTRON
SBS	Chr1	24935853	C-T	Homo	INTERGENIC
SBS	Chr1	40707606	G-A	Hetero	INTRON
SBS	Chr2	30626549	T-A	Hetero	INTERGENIC
SBS	Chr3	4638757	G-A	Hetero	INTERGENIC
SBS	Chr3	21340057	C-T	Homo	INTERGENIC
SBS	Chr3	23916477	C-T	Homo	INTERGENIC
SBS	Chr3	31305442	C-T	Homo	INTRON
SBS	Chr4	3291344	C-T	Hetero	INTERGENIC
SBS	Chr4	11317275	C-A	Hetero	INTERGENIC
SBS	Chr4	17760283	A-G	Hetero	INTERGENIC
SBS	Chr4	21359279	G-A	Hetero	INTERGENIC
SBS	Chr5	5883624	A-G	Hetero	INTERGENIC
SBS	Chr5	12814724	G-A	Hetero	INTERGENIC
SBS	Chr5	14218497	G-T	Hetero	INTERGENIC
SBS	Chr5	17561498	G-A	Hetero	NON_SYNONYMOUS_CODING	OsKitaake05g134600
SBS	Chr5	27501906	T-G	Hetero	INTERGENIC
SBS	Chr5	28210889	G-A	Homo	NON_SYNONYMOUS_CODING	OsKitaake05g261400
SBS	Chr6	4883706	T-A	Hetero	INTERGENIC
SBS	Chr6	18387645	G-T	Hetero	INTERGENIC
SBS	Chr6	23883013	C-T	Hetero	INTERGENIC
SBS	Chr7	12158364	C-T	Homo	INTERGENIC
SBS	Chr8	9863145	G-A	Hetero	NON_SYNONYMOUS_CODING	OsKitaake08g091700
SBS	Chr8	14020210	G-A	Hetero	INTRON
SBS	Chr8	14843572	G-A	Hetero	INTERGENIC
SBS	Chr8	25667308	A-T	Homo	INTERGENIC
SBS	Chr8	26561489	A-T	Hetero	INTRON
SBS	Chr8	28421811	G-A	Hetero	INTERGENIC
SBS	Chr9	656573	C-T	Hetero	INTERGENIC
SBS	Chr9	3907507	C-T	Homo	INTERGENIC
SBS	Chr9	5139512	T-C	Hetero	INTERGENIC
SBS	Chr9	9755512	C-A	Hetero	INTRON
SBS	Chr9	19437079	G-T	Hetero	SYNONYMOUS_CODING
SBS	Chr9	19437080	G-T	Hetero	NON_SYNONYMOUS_CODING	OsKitaake09g158200
SBS	Chr9	22227353	G-A	Hetero	INTRON
SBS	Chr10	9880467	G-A	Hetero	INTRON
SBS	Chr10	11717773	A-C	Hetero	INTERGENIC
SBS	Chr10	15683704	A-T	Hetero	INTERGENIC
SBS	Chr11	11165539	C-A	Hetero	INTERGENIC
SBS	Chr11	14118919	G-A	Hetero	INTERGENIC
SBS	Chr11	15374394	C-A	Hetero	INTERGENIC
SBS	Chr11	17047646	A-G	Hetero	UTR_5_PRIME
SBS	Chr11	20466539	C-G	Hetero	INTRON
SBS	Chr11	26235508	G-A	Hetero	INTERGENIC
SBS	Chr12	5713474	T-G	Hetero	INTERGENIC
SBS	Chr12	6520054	G-A	Hetero	INTERGENIC
SBS	Chr12	7553514	T-C	Hetero	INTRON
SBS	Chr12	18434290	A-T	Homo	INTERGENIC
SBS	Chr12	18434291	G-T	Homo	INTERGENIC
SBS	Chr12	25940761	A-T	Homo	INTERGENIC

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr4	4760001	4953000	192999	4
Deletion	Chr8	5255001	5272000	16999	OsKitaake08g057000
Deletion	Chr7	5265280	5265281	1
Deletion	Chr8	10097126	10097128	2
Deletion	Chr9	10386447	10386448	1
Deletion	Chr4	10479001	10493000	13999
Deletion	Chr9	10996001	11046000	49999	6
Deletion	Chr7	11282046	11282048	2
Deletion	Chr7	12024001	12052000	27999
Deletion	Chr12	12588001	12617000	28999	5
Deletion	Chr1	17189332	17189497	165
Deletion	Chr1	17242104	17242106	2
Deletion	Chr12	18532428	18532431	3
Deletion	Chr7	19175786	19175789	3
Deletion	Chr12	19303969	19303980	11
Deletion	Chr5	21335001	21352000	16999	OsKitaake05g172900
Deletion	Chr1	21788083	21788089	6
Deletion	Chr7	22294867	22294874	7	OsKitaake07g188500
Deletion	Chr3	24761686	24761693	7
Deletion	Chr12	26732242	26732245	3
Deletion	Chr4	27590516	27590520	4
Deletion	Chr6	27684001	27703000	18999	OsKitaake06g250900
Deletion	Chr5	30223346	30223347	1
Deletion	Chr1	41343001	41361000	17999

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr11	8735266	8754055	OsKitaake11g094400
Inversion	Chr11	8754058	8791357
Inversion	Chr8	15276841	15506118	OsKitaake08g119200
Inversion	Chr8	15506106	15578855
Inversion	Chr1	41416022	41791232	OsKitaake01g457100
Inversion	Chr1	41416032	41791244	OsKitaake01g457100

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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