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Mutant Information

Mutant Name	FN3067-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN3067-S Alignment File
Seed Availability	Yes [Order Seeds]
Phenotype	TO:0000430 (Germination Rate) = Low (Between 25% and 75%) For more information, please see this phenotype file

Variant Information

Single base substitutions: 34

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 25591214 A-G Homo INTERGENIC
SBS Chr2 31488410 A-G Hetero INTERGENIC
SBS Chr3 1539899 T-A Hetero INTERGENIC
SBS Chr3 8089251 C-T Hetero UTR_5_PRIME
SBS Chr3 11612207 C-A Hetero INTERGENIC
SBS Chr3 20206531 A-T Hetero INTERGENIC
SBS Chr3 22684959 C-A Hetero INTRON
SBS Chr3 25777573 A-G Homo INTERGENIC
SBS Chr3 29089551 C-T Homo INTRON
SBS Chr3 35834681 A-G Hetero INTRON
SBS Chr4 20020805 A-C Hetero INTERGENIC
SBS Chr4 22814585 G-A Hetero INTERGENIC
SBS Chr4 32250833 G-A Homo INTERGENIC
SBS Chr5 140530 G-A Hetero INTERGENIC
SBS Chr5 5364128 A-T Homo INTERGENIC
SBS Chr5 7559467 G-A Homo INTERGENIC
SBS Chr5 16722817 T-A Hetero NON_SYNONYMOUS_CODING OsKitaake05g128100
SBS Chr5 24572494 C-A Homo INTERGENIC
SBS Chr5 24728982 A-G Homo INTERGENIC
SBS Chr6 22447878 C-T Hetero UTR_3_PRIME
SBS Chr7 20264186 T-C Hetero INTRON
SBS Chr7 20560516 T-C Hetero UTR_3_PRIME
SBS Chr7 23595623 A-T Hetero INTERGENIC
SBS Chr8 5257743 G-A Hetero INTERGENIC
SBS Chr8 5590155 G-A Hetero INTERGENIC
SBS Chr8 15026033 T-C Hetero NON_SYNONYMOUS_CODING OsKitaake08g117500
SBS Chr8 17269825 G-T Hetero INTERGENIC
SBS Chr9 2567453 G-A Hetero INTERGENIC
SBS Chr9 3177498 G-A Hetero INTERGENIC
SBS Chr9 7537801 G-T Hetero INTERGENIC
SBS Chr9 9981337 T-A Hetero INTERGENIC
SBS Chr11 14994984 A-T Hetero INTERGENIC
SBS Chr11 16120451 G-A Homo INTRON
SBS Chr12 6010528 C-T Hetero INTERGENIC

Deletions: 60

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr10 597001 612000 14999 OsKitaake10g004300
Deletion Chr1 781001 790000 8999 2
Deletion Chr11 965001 990000 24999 4
Deletion Chr11 1145001 1172000 26999 2
Deletion Chr2 1441001 1452000 10999 5
Deletion Chr3 2050125 2050128 3
Deletion Chr7 2772001 2789000 16999
Deletion Chr12 3527660 3527664 4
Deletion Chr1 3838001 3867000 28999
Deletion Chr7 4451001 4466000 14999 2
Deletion Chr10 5769001 5791000 21999 3
Deletion Chr12 6481001 6494000 12999 OsKitaake12g074500
Deletion Chr4 6971001 6982000 10999 OsKitaake04g035300
Deletion Chr8 7848001 7870000 21999
Deletion Chr11 8758001 8780000 21999
Deletion Chr12 9057067 9057069 2
Deletion Chr6 9339001 9351000 11999 2
Deletion Chr5 9388001 9404000 15999
Deletion Chr12 9939001 9957000 17999
Deletion Chr11 9976001 9989000 12999 OsKitaake11g101701
Deletion Chr11 10028001 10044000 15999 3
Deletion Chr5 10123001 10158000 34999 OsKitaake05g089901
Deletion Chr5 10196001 10470000 273999
Deletion Chr12 11379001 11401000 21999
Deletion Chr5 12640001 12690000 49999 OsKitaake05g098900
Deletion Chr9 13119001 13128000 8999
Deletion Chr1 13425001 13438000 12999 OsKitaake01g156400
Deletion Chr9 13609624 13609629 5
Deletion Chr12 13803001 13827000 23999
Deletion Chr10 13857388 13857399 11
Deletion Chr8 13876001 13888000 11999
Deletion Chr1 14222001 14234000 11999
Deletion Chr2 14514552 14514554 2
Deletion Chr3 14706001 14725000 18999 4
Deletion Chr2 14822001 14851000 28999
Deletion Chr2 14884001 14900000 15999 OsKitaake02g157500
Deletion Chr2 15177001 15186000 8999 OsKitaake02g158700
Deletion Chr12 15538001 15560000 21999 OsKitaake12g120600
Deletion Chr3 16010001 16027000 16999 2
Deletion Chr3 17010001 17023000 12999
Deletion Chr6 17736001 17748000 11999
Deletion Chr10 18084537 18084547 10
Deletion Chr8 18086001 18110000 23999 OsKitaake08g134500
Deletion Chr3 18679001 18712000 32999 OsKitaake03g225500
Deletion Chr2 18694001 18705000 10999 OsKitaake02g184000
Deletion Chr11 18905001 18923000 17999 OsKitaake11g147500
Deletion Chr8 19695001 19710000 14999
Deletion Chr11 20205001 20218000 12999
Deletion Chr4 20626259 20626263 4
Deletion Chr11 20779204 20779207 3
Deletion Chr1 20965001 20987000 21999 2
Deletion Chr10 22337039 22337047 8
Deletion Chr8 23537001 23550000 12999
Deletion Chr11 23581001 23592000 10999
Deletion Chr3 24775001 24803000 27999
Deletion Chr11 27291001 27300000 8999
Deletion Chr3 27324670 27324672 2
Deletion Chr3 31816142 31816154 12
Deletion Chr1 33167773 33167774 1
Deletion Chr1 39688340 39688348 8

Insertions: 5

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr2 1347710 1347713 2
Insertion Chr4 15932719 15932722 2
Insertion Chr9 5824731 5824734 2
Insertion Chr10 20427374 20427379 4
Insertion Chr7 11994714 11994716 1

Translocations: 5

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes

Translocation Chr5 10198942 Chr2 31447208
Translocation Chr8 14921963 Chr2 32978488 OsKitaake08g117000
Translocation Chr8 14922130 Chr2 32978489 OsKitaake08g117000
Translocation Chr3 23421237 Chr1 38568041
Translocation Chr3 23421253 Chr1 39577966

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	25591214	A-G	Homo	INTERGENIC
SBS	Chr2	31488410	A-G	Hetero	INTERGENIC
SBS	Chr3	1539899	T-A	Hetero	INTERGENIC
SBS	Chr3	8089251	C-T	Hetero	UTR_5_PRIME
SBS	Chr3	11612207	C-A	Hetero	INTERGENIC
SBS	Chr3	20206531	A-T	Hetero	INTERGENIC
SBS	Chr3	22684959	C-A	Hetero	INTRON
SBS	Chr3	25777573	A-G	Homo	INTERGENIC
SBS	Chr3	29089551	C-T	Homo	INTRON
SBS	Chr3	35834681	A-G	Hetero	INTRON
SBS	Chr4	20020805	A-C	Hetero	INTERGENIC
SBS	Chr4	22814585	G-A	Hetero	INTERGENIC
SBS	Chr4	32250833	G-A	Homo	INTERGENIC
SBS	Chr5	140530	G-A	Hetero	INTERGENIC
SBS	Chr5	5364128	A-T	Homo	INTERGENIC
SBS	Chr5	7559467	G-A	Homo	INTERGENIC
SBS	Chr5	16722817	T-A	Hetero	NON_SYNONYMOUS_CODING	OsKitaake05g128100
SBS	Chr5	24572494	C-A	Homo	INTERGENIC
SBS	Chr5	24728982	A-G	Homo	INTERGENIC
SBS	Chr6	22447878	C-T	Hetero	UTR_3_PRIME
SBS	Chr7	20264186	T-C	Hetero	INTRON
SBS	Chr7	20560516	T-C	Hetero	UTR_3_PRIME
SBS	Chr7	23595623	A-T	Hetero	INTERGENIC
SBS	Chr8	5257743	G-A	Hetero	INTERGENIC
SBS	Chr8	5590155	G-A	Hetero	INTERGENIC
SBS	Chr8	15026033	T-C	Hetero	NON_SYNONYMOUS_CODING	OsKitaake08g117500
SBS	Chr8	17269825	G-T	Hetero	INTERGENIC
SBS	Chr9	2567453	G-A	Hetero	INTERGENIC
SBS	Chr9	3177498	G-A	Hetero	INTERGENIC
SBS	Chr9	7537801	G-T	Hetero	INTERGENIC
SBS	Chr9	9981337	T-A	Hetero	INTERGENIC
SBS	Chr11	14994984	A-T	Hetero	INTERGENIC
SBS	Chr11	16120451	G-A	Homo	INTRON
SBS	Chr12	6010528	C-T	Hetero	INTERGENIC

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr10	597001	612000	14999	OsKitaake10g004300
Deletion	Chr1	781001	790000	8999	2
Deletion	Chr11	965001	990000	24999	4
Deletion	Chr11	1145001	1172000	26999	2
Deletion	Chr2	1441001	1452000	10999	5
Deletion	Chr3	2050125	2050128	3
Deletion	Chr7	2772001	2789000	16999
Deletion	Chr12	3527660	3527664	4
Deletion	Chr1	3838001	3867000	28999
Deletion	Chr7	4451001	4466000	14999	2
Deletion	Chr10	5769001	5791000	21999	3
Deletion	Chr12	6481001	6494000	12999	OsKitaake12g074500
Deletion	Chr4	6971001	6982000	10999	OsKitaake04g035300
Deletion	Chr8	7848001	7870000	21999
Deletion	Chr11	8758001	8780000	21999
Deletion	Chr12	9057067	9057069	2
Deletion	Chr6	9339001	9351000	11999	2
Deletion	Chr5	9388001	9404000	15999
Deletion	Chr12	9939001	9957000	17999
Deletion	Chr11	9976001	9989000	12999	OsKitaake11g101701
Deletion	Chr11	10028001	10044000	15999	3
Deletion	Chr5	10123001	10158000	34999	OsKitaake05g089901
Deletion	Chr5	10196001	10470000	273999
Deletion	Chr12	11379001	11401000	21999
Deletion	Chr5	12640001	12690000	49999	OsKitaake05g098900
Deletion	Chr9	13119001	13128000	8999
Deletion	Chr1	13425001	13438000	12999	OsKitaake01g156400
Deletion	Chr9	13609624	13609629	5
Deletion	Chr12	13803001	13827000	23999
Deletion	Chr10	13857388	13857399	11
Deletion	Chr8	13876001	13888000	11999
Deletion	Chr1	14222001	14234000	11999
Deletion	Chr2	14514552	14514554	2
Deletion	Chr3	14706001	14725000	18999	4
Deletion	Chr2	14822001	14851000	28999
Deletion	Chr2	14884001	14900000	15999	OsKitaake02g157500
Deletion	Chr2	15177001	15186000	8999	OsKitaake02g158700
Deletion	Chr12	15538001	15560000	21999	OsKitaake12g120600
Deletion	Chr3	16010001	16027000	16999	2
Deletion	Chr3	17010001	17023000	12999
Deletion	Chr6	17736001	17748000	11999
Deletion	Chr10	18084537	18084547	10
Deletion	Chr8	18086001	18110000	23999	OsKitaake08g134500
Deletion	Chr3	18679001	18712000	32999	OsKitaake03g225500
Deletion	Chr2	18694001	18705000	10999	OsKitaake02g184000
Deletion	Chr11	18905001	18923000	17999	OsKitaake11g147500
Deletion	Chr8	19695001	19710000	14999
Deletion	Chr11	20205001	20218000	12999
Deletion	Chr4	20626259	20626263	4
Deletion	Chr11	20779204	20779207	3
Deletion	Chr1	20965001	20987000	21999	2
Deletion	Chr10	22337039	22337047	8
Deletion	Chr8	23537001	23550000	12999
Deletion	Chr11	23581001	23592000	10999
Deletion	Chr3	24775001	24803000	27999
Deletion	Chr11	27291001	27300000	8999
Deletion	Chr3	27324670	27324672	2
Deletion	Chr3	31816142	31816154	12
Deletion	Chr1	33167773	33167774	1
Deletion	Chr1	39688340	39688348	8

Variant Type	Chromosome	Position 1	Chromosome	Position 2	Number of Genes
Translocation	Chr5	10198942	Chr2	31447208
Translocation	Chr8	14921963	Chr2	32978488	OsKitaake08g117000
Translocation	Chr8	14922130	Chr2	32978489	OsKitaake08g117000
Translocation	Chr3	23421237	Chr1	38568041
Translocation	Chr3	23421253	Chr1	39577966

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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