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Mutant Information

Mutant Name	FN1429-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN1429-S Alignment File
Seed Availability	Yes [Order Seeds]
Phenotype	TO:0000014 (Panicle Weight) = Low (Between 25% and 74%) TO:0000207 (Plant height) = Normal (Between 75% and 125%) TO:0000445 (Seed Number) = Low (Between 25% and 74%) TO:0000639 (Seed fertility) = 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 8021403 G-A Hetero INTRON
SBS Chr1 34813643 C-T Hetero INTRON
SBS Chr2 856556 C-T Homo INTERGENIC
SBS Chr3 6450728 T-A Homo INTRON
SBS Chr3 15352225 G-A Hetero INTERGENIC
SBS Chr3 22219954 C-T Hetero INTERGENIC
SBS Chr3 28619093 A-C Hetero INTERGENIC
SBS Chr3 36629104 A-T Hetero INTERGENIC
SBS Chr4 12990857 T-A Homo UTR_5_PRIME
SBS Chr4 30237086 A-T Hetero INTERGENIC
SBS Chr5 3705992 T-C Hetero INTRON
SBS Chr5 13374756 C-A Hetero INTERGENIC
SBS Chr5 13374757 T-A Hetero INTERGENIC
SBS Chr5 28175934 G-A Homo NON_SYNONYMOUS_CODING OsKitaake05g261000
SBS Chr7 24128318 G-T Hetero NON_SYNONYMOUS_CODING OsKitaake07g214000
SBS Chr8 5274000 T-A Homo INTRON
SBS Chr8 13324655 C-A Hetero INTERGENIC
SBS Chr9 21710120 T-G Hetero INTERGENIC
SBS Chr10 4242299 T-A Hetero INTERGENIC
SBS Chr10 4242300 C-A Hetero INTERGENIC
SBS Chr10 17750807 C-T Homo INTERGENIC
SBS Chr11 2747670 T-C Hetero INTERGENIC
SBS Chr11 13782825 G-A Hetero INTERGENIC
SBS Chr11 15157617 A-T Hetero INTRON
SBS Chr11 15157618 A-T Hetero INTRON
SBS Chr11 15951382 A-G Homo INTERGENIC
SBS Chr11 26381035 T-C Homo INTERGENIC
SBS Chr11 28238749 C-G Hetero INTERGENIC
SBS Chr12 3111185 G-T Hetero INTERGENIC
SBS Chr12 5290505 C-A Hetero INTERGENIC
SBS Chr12 8149624 C-A Hetero INTERGENIC
SBS Chr12 16243571 T-A Hetero INTERGENIC
SBS Chr12 16243578 T-G Hetero INTERGENIC
SBS Chr12 16450697 C-T Hetero INTERGENIC
SBS Chr12 18512690 T-G Hetero INTRON

Deletions: 85

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr7 1001 10000 8999
Deletion Chr3 166001 185000 18999 4
Deletion Chr8 918001 938000 19999 OsKitaake08g012200
Deletion Chr7 1653001 1672000 18999 6
Deletion Chr2 2104001 2117000 12999 2
Deletion Chr1 2229001 2258000 28999 2
Deletion Chr7 2525001 2536000 10999 OsKitaake07g033700
Deletion Chr2 3336001 3348000 11999
Deletion Chr5 3373001 3382000 8999 OsKitaake05g040700
Deletion Chr2 3379001 3397000 17999 OsKitaake02g048900
Deletion Chr1 3636001 3660000 23999 2
Deletion Chr6 3825001 3832000 6999 2
Deletion Chr7 3941001 3962000 20999 2
Deletion Chr1 4466001 4483000 16999 OsKitaake01g059500
Deletion Chr8 4521001 4545000 23999 2
Deletion Chr2 4574001 4590000 15999 3
Deletion Chr8 4602001 4612000 9999 OsKitaake08g052000
Deletion Chr7 4741001 4755000 13999
Deletion Chr8 5295001 5310000 14999 3
Deletion Chr2 5798001 5823000 24999 2
Deletion Chr7 6223001 6233000 9999 2
Deletion Chr4 6461860 6461875 15
Deletion Chr9 6740001 6759000 18999 2
Deletion Chr11 7002001 7016000 13999 OsKitaake11g080300
Deletion Chr12 7145001 7163000 17999 OsKitaake12g080100
Deletion Chr8 7858001 7872000 13999
Deletion Chr7 9014001 9026000 11999 2
Deletion Chr7 9052001 9067000 14999 OsKitaake07g095000
Deletion Chr9 9624001 9634000 9999 OsKitaake09g058700
Deletion Chr6 11483001 11495000 11999 OsKitaake06g126800
Deletion Chr7 12021001 12033000 11999
Deletion Chr2 12159001 12173000 13999 2
Deletion Chr4 12316001 12329000 12999 4
Deletion Chr12 13359001 13372000 12999 OsKitaake12g111100
Deletion Chr9 13363001 13377000 13999 2
Deletion Chr3 13420001 13433000 12999 OsKitaake03g179400
Deletion Chr9 14237001 14248000 10999 OsKitaake09g095800
Deletion Chr1 14672001 14699000 26999 OsKitaake01g166200
Deletion Chr1 15000982 15000994 12
Deletion Chr2 15416001 15426000 9999
Deletion Chr5 15781001 15793000 11999 OsKitaake05g121500
Deletion Chr4 15979593 15979594 1
Deletion Chr5 16277001 16289000 11999 OsKitaake05g124400
Deletion Chr2 16308001 16325000 16999 OsKitaake02g167700
Deletion Chr2 16348001 16359000 10999 OsKitaake02g167800
Deletion Chr12 16707700 16707704 4
Deletion Chr2 16872679 16872681 2
Deletion Chr12 17305001 17318000 12999 OsKitaake12g127300
Deletion Chr4 17492149 17492171 22
Deletion Chr8 17844001 17851000 6999 OsKitaake08g133400
Deletion Chr11 18498001 18508000 9999 OsKitaake11g143100
Deletion Chr5 19093001 19114000 20999 2
Deletion Chr7 19211001 19226000 14999 3
Deletion Chr12 19340001 19355000 14999 2
Deletion Chr1 19671001 19685000 13999 OsKitaake01g196000
Deletion Chr8 22620001 22633000 12999 OsKitaake08g173500
Deletion Chr10 22687001 22699000 11999 OsKitaake10g187800
Deletion Chr12 23125001 23137000 11999 OsKitaake12g184500
Deletion Chr12 23447001 23462000 14999 OsKitaake12g187900
Deletion Chr1 23740001 23777000 36999 3
Deletion Chr12 23808001 23820000 11999 OsKitaake12g191766
Deletion Chr12 23853001 23866000 12999 OsKitaake12g192200
Deletion Chr12 23920001 23937000 16999 OsKitaake12g192700
Deletion Chr6 24010001 24049000 38999 OsKitaake06g213000
Deletion Chr11 25113001 25125000 11999 2
Deletion Chr6 25257001 25275000 17999 OsKitaake06g223800
Deletion Chr12 25498201 25498203 2
Deletion Chr1 25826104 25826114 10
Deletion Chr12 26042001 26064000 21999 2
Deletion Chr12 27128001 27137000 8999 OsKitaake12g228600
Deletion Chr12 27141001 27154000 12999
Deletion Chr7 27669001 27690000 20999 2
Deletion Chr5 27748001 27758000 9999 OsKitaake05g254100
Deletion Chr1 28147001 28159000 11999 3
Deletion Chr5 28174891 28174896 5 OsKitaake05g261000
Deletion Chr3 28185001 28208000 22999 2
Deletion Chr1 29485001 29498000 12999 OsKitaake01g289000
Deletion Chr7 29656001 29684000 27999
Deletion Chr5 30042001 30053000 10999 OsKitaake05g288400
Deletion Chr3 30732101 30732105 4
Deletion Chr2 32161001 32187000 25999 2
Deletion Chr4 32814001 32836000 21999 3
Deletion Chr1 35777001 35788000 10999 3
Deletion Chr2 37113001 37185000 71999 5
Deletion Chr1 41465001 41480000 14999

Insertions: 2

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr1 19737435 19737440 4
Insertion Chr1 23284336 23284340 3

Inversions: 4

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Inversion Chr7 8820657 8822222
Inversion Chr12 9073543 9552034
Inversion Chr12 25659160 25680609 OsKitaake12g211800
Inversion Chr12 25659325 25680628 OsKitaake12g211800

Translocations: 8

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes

Translocation Chr12 3999775 Chr4 24596870
Translocation Chr9 4325556 Chr3 28619186
Translocation Chr9 4325558 Chr3 28619577
Translocation Chr12 9073530 Chr2 37113017
Translocation Chr10 13581804 Chr7 24018989
Translocation Chr11 15549160 Chr1 3873305
Translocation Chr11 15549163 Chr1 3863701
Translocation Chr4 35451499 Chr2 37113011 OsKitaake04g300700

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	8021403	G-A	Hetero	INTRON
SBS	Chr1	34813643	C-T	Hetero	INTRON
SBS	Chr2	856556	C-T	Homo	INTERGENIC
SBS	Chr3	6450728	T-A	Homo	INTRON
SBS	Chr3	15352225	G-A	Hetero	INTERGENIC
SBS	Chr3	22219954	C-T	Hetero	INTERGENIC
SBS	Chr3	28619093	A-C	Hetero	INTERGENIC
SBS	Chr3	36629104	A-T	Hetero	INTERGENIC
SBS	Chr4	12990857	T-A	Homo	UTR_5_PRIME
SBS	Chr4	30237086	A-T	Hetero	INTERGENIC
SBS	Chr5	3705992	T-C	Hetero	INTRON
SBS	Chr5	13374756	C-A	Hetero	INTERGENIC
SBS	Chr5	13374757	T-A	Hetero	INTERGENIC
SBS	Chr5	28175934	G-A	Homo	NON_SYNONYMOUS_CODING	OsKitaake05g261000
SBS	Chr7	24128318	G-T	Hetero	NON_SYNONYMOUS_CODING	OsKitaake07g214000
SBS	Chr8	5274000	T-A	Homo	INTRON
SBS	Chr8	13324655	C-A	Hetero	INTERGENIC
SBS	Chr9	21710120	T-G	Hetero	INTERGENIC
SBS	Chr10	4242299	T-A	Hetero	INTERGENIC
SBS	Chr10	4242300	C-A	Hetero	INTERGENIC
SBS	Chr10	17750807	C-T	Homo	INTERGENIC
SBS	Chr11	2747670	T-C	Hetero	INTERGENIC
SBS	Chr11	13782825	G-A	Hetero	INTERGENIC
SBS	Chr11	15157617	A-T	Hetero	INTRON
SBS	Chr11	15157618	A-T	Hetero	INTRON
SBS	Chr11	15951382	A-G	Homo	INTERGENIC
SBS	Chr11	26381035	T-C	Homo	INTERGENIC
SBS	Chr11	28238749	C-G	Hetero	INTERGENIC
SBS	Chr12	3111185	G-T	Hetero	INTERGENIC
SBS	Chr12	5290505	C-A	Hetero	INTERGENIC
SBS	Chr12	8149624	C-A	Hetero	INTERGENIC
SBS	Chr12	16243571	T-A	Hetero	INTERGENIC
SBS	Chr12	16243578	T-G	Hetero	INTERGENIC
SBS	Chr12	16450697	C-T	Hetero	INTERGENIC
SBS	Chr12	18512690	T-G	Hetero	INTRON

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr7	1001	10000	8999
Deletion	Chr3	166001	185000	18999	4
Deletion	Chr8	918001	938000	19999	OsKitaake08g012200
Deletion	Chr7	1653001	1672000	18999	6
Deletion	Chr2	2104001	2117000	12999	2
Deletion	Chr1	2229001	2258000	28999	2
Deletion	Chr7	2525001	2536000	10999	OsKitaake07g033700
Deletion	Chr2	3336001	3348000	11999
Deletion	Chr5	3373001	3382000	8999	OsKitaake05g040700
Deletion	Chr2	3379001	3397000	17999	OsKitaake02g048900
Deletion	Chr1	3636001	3660000	23999	2
Deletion	Chr6	3825001	3832000	6999	2
Deletion	Chr7	3941001	3962000	20999	2
Deletion	Chr1	4466001	4483000	16999	OsKitaake01g059500
Deletion	Chr8	4521001	4545000	23999	2
Deletion	Chr2	4574001	4590000	15999	3
Deletion	Chr8	4602001	4612000	9999	OsKitaake08g052000
Deletion	Chr7	4741001	4755000	13999
Deletion	Chr8	5295001	5310000	14999	3
Deletion	Chr2	5798001	5823000	24999	2
Deletion	Chr7	6223001	6233000	9999	2
Deletion	Chr4	6461860	6461875	15
Deletion	Chr9	6740001	6759000	18999	2
Deletion	Chr11	7002001	7016000	13999	OsKitaake11g080300
Deletion	Chr12	7145001	7163000	17999	OsKitaake12g080100
Deletion	Chr8	7858001	7872000	13999
Deletion	Chr7	9014001	9026000	11999	2
Deletion	Chr7	9052001	9067000	14999	OsKitaake07g095000
Deletion	Chr9	9624001	9634000	9999	OsKitaake09g058700
Deletion	Chr6	11483001	11495000	11999	OsKitaake06g126800
Deletion	Chr7	12021001	12033000	11999
Deletion	Chr2	12159001	12173000	13999	2
Deletion	Chr4	12316001	12329000	12999	4
Deletion	Chr12	13359001	13372000	12999	OsKitaake12g111100
Deletion	Chr9	13363001	13377000	13999	2
Deletion	Chr3	13420001	13433000	12999	OsKitaake03g179400
Deletion	Chr9	14237001	14248000	10999	OsKitaake09g095800
Deletion	Chr1	14672001	14699000	26999	OsKitaake01g166200
Deletion	Chr1	15000982	15000994	12
Deletion	Chr2	15416001	15426000	9999
Deletion	Chr5	15781001	15793000	11999	OsKitaake05g121500
Deletion	Chr4	15979593	15979594	1
Deletion	Chr5	16277001	16289000	11999	OsKitaake05g124400
Deletion	Chr2	16308001	16325000	16999	OsKitaake02g167700
Deletion	Chr2	16348001	16359000	10999	OsKitaake02g167800
Deletion	Chr12	16707700	16707704	4
Deletion	Chr2	16872679	16872681	2
Deletion	Chr12	17305001	17318000	12999	OsKitaake12g127300
Deletion	Chr4	17492149	17492171	22
Deletion	Chr8	17844001	17851000	6999	OsKitaake08g133400
Deletion	Chr11	18498001	18508000	9999	OsKitaake11g143100
Deletion	Chr5	19093001	19114000	20999	2
Deletion	Chr7	19211001	19226000	14999	3
Deletion	Chr12	19340001	19355000	14999	2
Deletion	Chr1	19671001	19685000	13999	OsKitaake01g196000
Deletion	Chr8	22620001	22633000	12999	OsKitaake08g173500
Deletion	Chr10	22687001	22699000	11999	OsKitaake10g187800
Deletion	Chr12	23125001	23137000	11999	OsKitaake12g184500
Deletion	Chr12	23447001	23462000	14999	OsKitaake12g187900
Deletion	Chr1	23740001	23777000	36999	3
Deletion	Chr12	23808001	23820000	11999	OsKitaake12g191766
Deletion	Chr12	23853001	23866000	12999	OsKitaake12g192200
Deletion	Chr12	23920001	23937000	16999	OsKitaake12g192700
Deletion	Chr6	24010001	24049000	38999	OsKitaake06g213000
Deletion	Chr11	25113001	25125000	11999	2
Deletion	Chr6	25257001	25275000	17999	OsKitaake06g223800
Deletion	Chr12	25498201	25498203	2
Deletion	Chr1	25826104	25826114	10
Deletion	Chr12	26042001	26064000	21999	2
Deletion	Chr12	27128001	27137000	8999	OsKitaake12g228600
Deletion	Chr12	27141001	27154000	12999
Deletion	Chr7	27669001	27690000	20999	2
Deletion	Chr5	27748001	27758000	9999	OsKitaake05g254100
Deletion	Chr1	28147001	28159000	11999	3
Deletion	Chr5	28174891	28174896	5	OsKitaake05g261000
Deletion	Chr3	28185001	28208000	22999	2
Deletion	Chr1	29485001	29498000	12999	OsKitaake01g289000
Deletion	Chr7	29656001	29684000	27999
Deletion	Chr5	30042001	30053000	10999	OsKitaake05g288400
Deletion	Chr3	30732101	30732105	4
Deletion	Chr2	32161001	32187000	25999	2
Deletion	Chr4	32814001	32836000	21999	3
Deletion	Chr1	35777001	35788000	10999	3
Deletion	Chr2	37113001	37185000	71999	5
Deletion	Chr1	41465001	41480000	14999

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr7	8820657	8822222
Inversion	Chr12	9073543	9552034
Inversion	Chr12	25659160	25680609	OsKitaake12g211800
Inversion	Chr12	25659325	25680628	OsKitaake12g211800

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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