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Mutant Information

Mutant Name	W416-6-1 [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download W416-6-1 Alignment File
Seed Availability	Yes [Order Seeds]
Phenotype	TO:0000430 (Germination Rate) = Normal (Between 75% and 125%) For more information, please see this phenotype file

Variant Information

Single base substitutions: 37

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 3086093 G-A Homo START_GAINED
SBS Chr1 33384421 T-A Homo SYNONYMOUS_CODING
SBS Chr1 37449059 C-A Homo INTERGENIC
SBS Chr2 523156 G-A Hetero SYNONYMOUS_CODING
SBS Chr2 9736890 C-T Homo INTERGENIC
SBS Chr2 17555525 G-A Hetero INTRON
SBS Chr2 31136354 A-G Hetero INTERGENIC
SBS Chr2 33551999 A-T Hetero INTERGENIC
SBS Chr3 14148613 T-A Hetero INTRON
SBS Chr3 18822395 T-A Homo INTERGENIC
SBS Chr3 18822396 C-T Homo INTERGENIC
SBS Chr4 7548848 G-A Hetero INTERGENIC
SBS Chr4 10032094 C-T Homo INTERGENIC
SBS Chr4 17020178 G-C Hetero INTERGENIC
SBS Chr5 27177520 G-A Hetero INTRON
SBS Chr5 27177521 C-A Hetero INTRON
SBS Chr6 6680629 G-A Hetero INTERGENIC
SBS Chr6 10825295 C-A Hetero INTERGENIC
SBS Chr6 19303871 G-A Hetero INTERGENIC
SBS Chr6 22994648 A-G Homo INTERGENIC
SBS Chr6 28931112 G-C Hetero NON_SYNONYMOUS_CODING OsKitaake06g267300
SBS Chr7 12042491 G-C Hetero INTERGENIC
SBS Chr7 19277452 G-A Hetero INTERGENIC
SBS Chr8 2579342 A-G Hetero INTERGENIC
SBS Chr8 3835949 G-A Homo INTERGENIC
SBS Chr8 13540120 C-T Hetero INTERGENIC
SBS Chr8 14377718 A-C Homo INTRON
SBS Chr8 14468485 A-G Homo INTERGENIC
SBS Chr8 18404393 A-T Homo INTERGENIC
SBS Chr9 902003 G-T Hetero INTERGENIC
SBS Chr9 3281662 T-A Homo INTRON
SBS Chr9 3462420 A-G Homo NON_SYNONYMOUS_CODING OsKitaake09g017701
SBS Chr9 13799072 A-C Hetero INTERGENIC
SBS Chr10 4601030 T-C Hetero INTERGENIC
SBS Chr10 15453310 G-A Homo INTERGENIC
SBS Chr12 1132279 G-T Homo NON_SYNONYMOUS_CODING OsKitaake12g016600
SBS Chr12 13440498 G-C Hetero INTRON

Deletions: 13

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr3 124564 124572 8
Deletion Chr12 760323 760325 2 OsKitaake12g010700
Deletion Chr1 5025391 5025394 3
Deletion Chr7 10531001 10545000 13999
Deletion Chr5 12028676 12028678 2
Deletion Chr9 12154206 12154208 2 OsKitaake09g078700
Deletion Chr5 15501631 15501632 1
Deletion Chr3 16214000 16214085 85
Deletion Chr8 18120198 18120207 9
Deletion Chr9 18516402 18516403 1 OsKitaake09g145400
Deletion Chr6 29036070 29036071 1
Deletion Chr6 29435054 29435062 8
Deletion Chr4 30497212 30497215 3

Insertions: 3

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr5 29401543 29401546 2
Insertion Chr10 20246017 20246022 4
Insertion Chr2 35354679 35354681 1

Inversions: 1

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Inversion Chr7 6334846 7131811

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	3086093	G-A	Homo	START_GAINED
SBS	Chr1	33384421	T-A	Homo	SYNONYMOUS_CODING
SBS	Chr1	37449059	C-A	Homo	INTERGENIC
SBS	Chr2	523156	G-A	Hetero	SYNONYMOUS_CODING
SBS	Chr2	9736890	C-T	Homo	INTERGENIC
SBS	Chr2	17555525	G-A	Hetero	INTRON
SBS	Chr2	31136354	A-G	Hetero	INTERGENIC
SBS	Chr2	33551999	A-T	Hetero	INTERGENIC
SBS	Chr3	14148613	T-A	Hetero	INTRON
SBS	Chr3	18822395	T-A	Homo	INTERGENIC
SBS	Chr3	18822396	C-T	Homo	INTERGENIC
SBS	Chr4	7548848	G-A	Hetero	INTERGENIC
SBS	Chr4	10032094	C-T	Homo	INTERGENIC
SBS	Chr4	17020178	G-C	Hetero	INTERGENIC
SBS	Chr5	27177520	G-A	Hetero	INTRON
SBS	Chr5	27177521	C-A	Hetero	INTRON
SBS	Chr6	6680629	G-A	Hetero	INTERGENIC
SBS	Chr6	10825295	C-A	Hetero	INTERGENIC
SBS	Chr6	19303871	G-A	Hetero	INTERGENIC
SBS	Chr6	22994648	A-G	Homo	INTERGENIC
SBS	Chr6	28931112	G-C	Hetero	NON_SYNONYMOUS_CODING	OsKitaake06g267300
SBS	Chr7	12042491	G-C	Hetero	INTERGENIC
SBS	Chr7	19277452	G-A	Hetero	INTERGENIC
SBS	Chr8	2579342	A-G	Hetero	INTERGENIC
SBS	Chr8	3835949	G-A	Homo	INTERGENIC
SBS	Chr8	13540120	C-T	Hetero	INTERGENIC
SBS	Chr8	14377718	A-C	Homo	INTRON
SBS	Chr8	14468485	A-G	Homo	INTERGENIC
SBS	Chr8	18404393	A-T	Homo	INTERGENIC
SBS	Chr9	902003	G-T	Hetero	INTERGENIC
SBS	Chr9	3281662	T-A	Homo	INTRON
SBS	Chr9	3462420	A-G	Homo	NON_SYNONYMOUS_CODING	OsKitaake09g017701
SBS	Chr9	13799072	A-C	Hetero	INTERGENIC
SBS	Chr10	4601030	T-C	Hetero	INTERGENIC
SBS	Chr10	15453310	G-A	Homo	INTERGENIC
SBS	Chr12	1132279	G-T	Homo	NON_SYNONYMOUS_CODING	OsKitaake12g016600
SBS	Chr12	13440498	G-C	Hetero	INTRON

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr3	124564	124572	8
Deletion	Chr12	760323	760325	2	OsKitaake12g010700
Deletion	Chr1	5025391	5025394	3
Deletion	Chr7	10531001	10545000	13999
Deletion	Chr5	12028676	12028678	2
Deletion	Chr9	12154206	12154208	2	OsKitaake09g078700
Deletion	Chr5	15501631	15501632	1
Deletion	Chr3	16214000	16214085	85
Deletion	Chr8	18120198	18120207	9
Deletion	Chr9	18516402	18516403	1	OsKitaake09g145400
Deletion	Chr6	29036070	29036071	1
Deletion	Chr6	29435054	29435062	8
Deletion	Chr4	30497212	30497215	3

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr7	6334846	7131811

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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