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Mutant Information

Mutant Name	FN1477-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN1477-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: 38

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 349019 G-C Hetero INTERGENIC
SBS Chr1 8724550 T-A Hetero INTERGENIC
SBS Chr1 22664768 G-A Hetero SYNONYMOUS_CODING
SBS Chr1 25150762 G-A Hetero INTERGENIC
SBS Chr1 43127602 T-G Homo INTERGENIC
SBS Chr2 2079713 C-A Homo UTR_3_PRIME
SBS Chr2 9062321 T-C Hetero INTERGENIC
SBS Chr2 12671286 G-A Hetero INTERGENIC
SBS Chr2 19679962 G-A Hetero INTERGENIC
SBS Chr3 1163822 A-T Hetero INTERGENIC
SBS Chr3 3817012 G-A Hetero UTR_5_PRIME
SBS Chr3 13494152 G-A Hetero INTERGENIC
SBS Chr3 14011895 T-A Hetero INTERGENIC
SBS Chr3 33143639 A-G Hetero UTR_5_PRIME
SBS Chr4 10266480 A-G Hetero INTERGENIC
SBS Chr4 11882010 C-T Hetero INTERGENIC
SBS Chr4 16001651 A-C Hetero INTERGENIC
SBS Chr4 27442142 G-A Hetero INTERGENIC
SBS Chr6 10501378 T-C Hetero INTERGENIC
SBS Chr6 12776461 A-T Hetero INTERGENIC
SBS Chr6 19319600 C-G Hetero INTERGENIC
SBS Chr7 9169399 A-G Hetero INTERGENIC
SBS Chr7 9592552 A-C Hetero INTERGENIC
SBS Chr7 24590884 G-A Hetero INTERGENIC
SBS Chr7 28333946 G-A Hetero SYNONYMOUS_CODING
SBS Chr8 2654683 T-G Homo INTERGENIC
SBS Chr8 7134451 A-G Hetero INTERGENIC
SBS Chr8 8952882 C-T Hetero INTERGENIC
SBS Chr8 13310904 C-T Hetero INTERGENIC
SBS Chr8 18028343 G-A Hetero INTERGENIC
SBS Chr9 8161331 A-G Hetero INTERGENIC
SBS Chr10 3095380 C-A Hetero INTERGENIC
SBS Chr10 5828488 G-A Hetero INTERGENIC
SBS Chr10 18324000 G-A Hetero INTERGENIC
SBS Chr11 5730152 A-C Hetero UTR_3_PRIME
SBS Chr11 25377364 C-T Hetero INTERGENIC
SBS Chr12 6726225 C-A Hetero INTERGENIC
SBS Chr12 18746209 A-G Homo NON_SYNONYMOUS_CODING OsKitaake12g138500

Deletions: 56

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr1 354001 384000 29999 OsKitaake01g005200
Deletion Chr7 498056 498057 1 OsKitaake07g005000
Deletion Chr6 761001 769000 7999 OsKitaake06g007600
Deletion Chr8 915001 950000 34999 3
Deletion Chr2 1629001 1651000 21999 4
Deletion Chr10 2250030 2250039 9
Deletion Chr2 2362001 2383000 20999 2
Deletion Chr10 2465724 2465727 3
Deletion Chr3 2525001 2538000 12999 OsKitaake03g035600
Deletion Chr2 3439001 3458000 18999 OsKitaake02g050200
Deletion Chr6 4091001 4102000 10999 OsKitaake06g057500
Deletion Chr1 4467001 4479000 11999 OsKitaake01g059500
Deletion Chr8 4979658 4979659 1
Deletion Chr8 5876001 5881000 4999 OsKitaake08g064100
Deletion Chr7 5989001 6005000 15999 OsKitaake07g072200
Deletion Chr6 6022001 6038000 15999 2
Deletion Chr12 7155001 7163000 7999 OsKitaake12g080100
Deletion Chr8 7724001 7732000 7999 OsKitaake08g071000
Deletion Chr2 7935001 7997000 61999 2
Deletion Chr3 8121030 8121032 2
Deletion Chr2 8603001 8613000 9999 OsKitaake02g109400
Deletion Chr1 10116955 10116956 1
Deletion Chr7 10604835 10604836 1
Deletion Chr12 10953001 10962000 8999 OsKitaake12g101500
Deletion Chr1 11189001 11203000 13999 OsKitaake01g137600
Deletion Chr5 12025249 12025259 10
Deletion Chr6 12338826 12338828 2
Deletion Chr1 14679001 14693000 13999 OsKitaake01g166200
Deletion Chr5 16795001 16803000 7999 OsKitaake05g128600
Deletion Chr10 17477001 17506000 28999 2
Deletion Chr10 17551001 17565000 13999 OsKitaake10g120000
Deletion Chr8 18963875 18963876 1
Deletion Chr10 19279001 19306000 26999 5
Deletion Chr11 20382001 20411000 28999 3
Deletion Chr2 21904001 21911000 6999
Deletion Chr9 22336001 22355000 18999 2
Deletion Chr11 22569001 22582000 12999 2
Deletion Chr7 22888001 22937000 48999 4
Deletion Chr10 23133001 23164000 30999 OsKitaake10g195250
Deletion Chr1 23253001 23272000 18999 OsKitaake01g222400
Deletion Chr12 24075023 24075045 22
Deletion Chr2 25965860 25965861 1
Deletion Chr8 26278665 26278675 10
Deletion Chr2 26298992 26298993 1
Deletion Chr8 26354001 26367000 12999 2
Deletion Chr5 27232256 27232261 5
Deletion Chr6 27912001 27934000 21999 3
Deletion Chr8 28140001 28163000 22999 4
Deletion Chr3 28583001 28597000 13999 OsKitaake03g296500
Deletion Chr7 29272001 29295000 22999 3
Deletion Chr1 33375001 33398000 22999 OsKitaake01g341200
Deletion Chr2 33798001 33804000 5999 OsKitaake02g349900
Deletion Chr3 34833001 34843000 9999 OsKitaake03g380100
Deletion Chr3 35335001 35347000 11999 OsKitaake03g387600
Deletion Chr1 36304001 36312000 7999
Deletion Chr1 41004001 41015000 10999 OsKitaake01g447600

Insertions: 2

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr5 15759739 15759741 1
Insertion Chr12 15209015 15209022 6

Inversions: 5

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Inversion Chr2 7779575 8007484 OsKitaake02g101700
Inversion Chr2 7779584 8621973 OsKitaake02g101700
Inversion Chr2 7943632 8621971
Inversion Chr2 7996743 8007491
Inversion Chr2 30918426 30925767

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	349019	G-C	Hetero	INTERGENIC
SBS	Chr1	8724550	T-A	Hetero	INTERGENIC
SBS	Chr1	22664768	G-A	Hetero	SYNONYMOUS_CODING
SBS	Chr1	25150762	G-A	Hetero	INTERGENIC
SBS	Chr1	43127602	T-G	Homo	INTERGENIC
SBS	Chr2	2079713	C-A	Homo	UTR_3_PRIME
SBS	Chr2	9062321	T-C	Hetero	INTERGENIC
SBS	Chr2	12671286	G-A	Hetero	INTERGENIC
SBS	Chr2	19679962	G-A	Hetero	INTERGENIC
SBS	Chr3	1163822	A-T	Hetero	INTERGENIC
SBS	Chr3	3817012	G-A	Hetero	UTR_5_PRIME
SBS	Chr3	13494152	G-A	Hetero	INTERGENIC
SBS	Chr3	14011895	T-A	Hetero	INTERGENIC
SBS	Chr3	33143639	A-G	Hetero	UTR_5_PRIME
SBS	Chr4	10266480	A-G	Hetero	INTERGENIC
SBS	Chr4	11882010	C-T	Hetero	INTERGENIC
SBS	Chr4	16001651	A-C	Hetero	INTERGENIC
SBS	Chr4	27442142	G-A	Hetero	INTERGENIC
SBS	Chr6	10501378	T-C	Hetero	INTERGENIC
SBS	Chr6	12776461	A-T	Hetero	INTERGENIC
SBS	Chr6	19319600	C-G	Hetero	INTERGENIC
SBS	Chr7	9169399	A-G	Hetero	INTERGENIC
SBS	Chr7	9592552	A-C	Hetero	INTERGENIC
SBS	Chr7	24590884	G-A	Hetero	INTERGENIC
SBS	Chr7	28333946	G-A	Hetero	SYNONYMOUS_CODING
SBS	Chr8	2654683	T-G	Homo	INTERGENIC
SBS	Chr8	7134451	A-G	Hetero	INTERGENIC
SBS	Chr8	8952882	C-T	Hetero	INTERGENIC
SBS	Chr8	13310904	C-T	Hetero	INTERGENIC
SBS	Chr8	18028343	G-A	Hetero	INTERGENIC
SBS	Chr9	8161331	A-G	Hetero	INTERGENIC
SBS	Chr10	3095380	C-A	Hetero	INTERGENIC
SBS	Chr10	5828488	G-A	Hetero	INTERGENIC
SBS	Chr10	18324000	G-A	Hetero	INTERGENIC
SBS	Chr11	5730152	A-C	Hetero	UTR_3_PRIME
SBS	Chr11	25377364	C-T	Hetero	INTERGENIC
SBS	Chr12	6726225	C-A	Hetero	INTERGENIC
SBS	Chr12	18746209	A-G	Homo	NON_SYNONYMOUS_CODING	OsKitaake12g138500

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr1	354001	384000	29999	OsKitaake01g005200
Deletion	Chr7	498056	498057	1	OsKitaake07g005000
Deletion	Chr6	761001	769000	7999	OsKitaake06g007600
Deletion	Chr8	915001	950000	34999	3
Deletion	Chr2	1629001	1651000	21999	4
Deletion	Chr10	2250030	2250039	9
Deletion	Chr2	2362001	2383000	20999	2
Deletion	Chr10	2465724	2465727	3
Deletion	Chr3	2525001	2538000	12999	OsKitaake03g035600
Deletion	Chr2	3439001	3458000	18999	OsKitaake02g050200
Deletion	Chr6	4091001	4102000	10999	OsKitaake06g057500
Deletion	Chr1	4467001	4479000	11999	OsKitaake01g059500
Deletion	Chr8	4979658	4979659	1
Deletion	Chr8	5876001	5881000	4999	OsKitaake08g064100
Deletion	Chr7	5989001	6005000	15999	OsKitaake07g072200
Deletion	Chr6	6022001	6038000	15999	2
Deletion	Chr12	7155001	7163000	7999	OsKitaake12g080100
Deletion	Chr8	7724001	7732000	7999	OsKitaake08g071000
Deletion	Chr2	7935001	7997000	61999	2
Deletion	Chr3	8121030	8121032	2
Deletion	Chr2	8603001	8613000	9999	OsKitaake02g109400
Deletion	Chr1	10116955	10116956	1
Deletion	Chr7	10604835	10604836	1
Deletion	Chr12	10953001	10962000	8999	OsKitaake12g101500
Deletion	Chr1	11189001	11203000	13999	OsKitaake01g137600
Deletion	Chr5	12025249	12025259	10
Deletion	Chr6	12338826	12338828	2
Deletion	Chr1	14679001	14693000	13999	OsKitaake01g166200
Deletion	Chr5	16795001	16803000	7999	OsKitaake05g128600
Deletion	Chr10	17477001	17506000	28999	2
Deletion	Chr10	17551001	17565000	13999	OsKitaake10g120000
Deletion	Chr8	18963875	18963876	1
Deletion	Chr10	19279001	19306000	26999	5
Deletion	Chr11	20382001	20411000	28999	3
Deletion	Chr2	21904001	21911000	6999
Deletion	Chr9	22336001	22355000	18999	2
Deletion	Chr11	22569001	22582000	12999	2
Deletion	Chr7	22888001	22937000	48999	4
Deletion	Chr10	23133001	23164000	30999	OsKitaake10g195250
Deletion	Chr1	23253001	23272000	18999	OsKitaake01g222400
Deletion	Chr12	24075023	24075045	22
Deletion	Chr2	25965860	25965861	1
Deletion	Chr8	26278665	26278675	10
Deletion	Chr2	26298992	26298993	1
Deletion	Chr8	26354001	26367000	12999	2
Deletion	Chr5	27232256	27232261	5
Deletion	Chr6	27912001	27934000	21999	3
Deletion	Chr8	28140001	28163000	22999	4
Deletion	Chr3	28583001	28597000	13999	OsKitaake03g296500
Deletion	Chr7	29272001	29295000	22999	3
Deletion	Chr1	33375001	33398000	22999	OsKitaake01g341200
Deletion	Chr2	33798001	33804000	5999	OsKitaake02g349900
Deletion	Chr3	34833001	34843000	9999	OsKitaake03g380100
Deletion	Chr3	35335001	35347000	11999	OsKitaake03g387600
Deletion	Chr1	36304001	36312000	7999
Deletion	Chr1	41004001	41015000	10999	OsKitaake01g447600

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr2	7779575	8007484	OsKitaake02g101700
Inversion	Chr2	7779584	8621973	OsKitaake02g101700
Inversion	Chr2	7943632	8621971
Inversion	Chr2	7996743	8007491
Inversion	Chr2	30918426	30925767

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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