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Mutant Information

SOS indicates the sequenced line is sterile and seeds from siblings are available.

Mutant Name	704-6 [Download]
Generation	M2-SOS
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download 704-6 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: 23

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 8546449 G-T Homo INTERGENIC
SBS Chr1 18151670 C-T Hetero INTERGENIC
SBS Chr2 27601254 T-A Hetero INTERGENIC
SBS Chr3 35818085 G-A Hetero NON_SYNONYMOUS_CODING OsKitaake03g394300
SBS Chr4 4840243 C-T Hetero INTERGENIC
SBS Chr4 23728438 G-A Homo INTRON
SBS Chr5 27161448 G-T Hetero INTERGENIC
SBS Chr5 28776652 T-A Hetero INTERGENIC
SBS Chr6 6073752 C-T Homo NON_SYNONYMOUS_CODING OsKitaake06g080000
SBS Chr6 10389318 A-T Hetero NON_SYNONYMOUS_CODING OsKitaake06g117600
SBS Chr6 21711980 T-A Hetero INTERGENIC
SBS Chr6 29980057 T-G Hetero INTERGENIC
SBS Chr7 6642187 T-A Homo NON_SYNONYMOUS_CODING OsKitaake07g076300
SBS Chr9 694461 G-T Hetero INTERGENIC
SBS Chr9 14631167 C-G Hetero INTRON
SBS Chr9 17331645 A-T Homo INTERGENIC
SBS Chr9 21387439 C-T Hetero INTERGENIC
SBS Chr10 581693 G-A Hetero INTERGENIC
SBS Chr11 27041408 C-T Hetero INTERGENIC
SBS Chr12 6289949 C-A Homo INTERGENIC
SBS Chr12 13929244 C-A Hetero INTERGENIC
SBS Chr12 18303754 G-A Homo INTERGENIC
SBS Chr12 24430260 C-T Hetero INTERGENIC

Deletions: 7

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr10 5197295 5197297 2
Deletion Chr8 5432526 5432528 2
Deletion Chr7 12417588 12417590 2 OsKitaake07g111000
Deletion Chr2 12864001 12876000 11999
Deletion Chr8 21359172 21359174 2 OsKitaake08g160200
Deletion Chr1 32791359 32791484 125
Deletion Chr3 33317898 33317899 1 OsKitaake03g355900

Insertions: 6

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr1 26680992 26680996 3
Insertion Chr2 18180096 18180098 1
Insertion Chr4 18297099 18297101 1
Insertion Chr4 18345247 18345250 2
Insertion Chr10 13199161 13199163 1
Insertion Chr10 21368120 21368123 2

Inversions: 2

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Inversion Chr6 10153005 10168170
Inversion Chr6 10153010 10168172

Translocations: 5

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes

Translocation Chr11 6916231 Chr6 5683072
Translocation Chr3 9397946 Chr2 12876192 OsKitaake03g127900
Translocation Chr9 10392826 Chr4 10517676
Translocation Chr9 10392835 Chr4 10518064
Translocation Chr6 21710743 Chr2 12863779 OsKitaake06g191400

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	8546449	G-T	Homo	INTERGENIC
SBS	Chr1	18151670	C-T	Hetero	INTERGENIC
SBS	Chr2	27601254	T-A	Hetero	INTERGENIC
SBS	Chr3	35818085	G-A	Hetero	NON_SYNONYMOUS_CODING	OsKitaake03g394300
SBS	Chr4	4840243	C-T	Hetero	INTERGENIC
SBS	Chr4	23728438	G-A	Homo	INTRON
SBS	Chr5	27161448	G-T	Hetero	INTERGENIC
SBS	Chr5	28776652	T-A	Hetero	INTERGENIC
SBS	Chr6	6073752	C-T	Homo	NON_SYNONYMOUS_CODING	OsKitaake06g080000
SBS	Chr6	10389318	A-T	Hetero	NON_SYNONYMOUS_CODING	OsKitaake06g117600
SBS	Chr6	21711980	T-A	Hetero	INTERGENIC
SBS	Chr6	29980057	T-G	Hetero	INTERGENIC
SBS	Chr7	6642187	T-A	Homo	NON_SYNONYMOUS_CODING	OsKitaake07g076300
SBS	Chr9	694461	G-T	Hetero	INTERGENIC
SBS	Chr9	14631167	C-G	Hetero	INTRON
SBS	Chr9	17331645	A-T	Homo	INTERGENIC
SBS	Chr9	21387439	C-T	Hetero	INTERGENIC
SBS	Chr10	581693	G-A	Hetero	INTERGENIC
SBS	Chr11	27041408	C-T	Hetero	INTERGENIC
SBS	Chr12	6289949	C-A	Homo	INTERGENIC
SBS	Chr12	13929244	C-A	Hetero	INTERGENIC
SBS	Chr12	18303754	G-A	Homo	INTERGENIC
SBS	Chr12	24430260	C-T	Hetero	INTERGENIC

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr10	5197295	5197297	2
Deletion	Chr8	5432526	5432528	2
Deletion	Chr7	12417588	12417590	2	OsKitaake07g111000
Deletion	Chr2	12864001	12876000	11999
Deletion	Chr8	21359172	21359174	2	OsKitaake08g160200
Deletion	Chr1	32791359	32791484	125
Deletion	Chr3	33317898	33317899	1	OsKitaake03g355900

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr6	10153005	10168170
Inversion	Chr6	10153010	10168172

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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