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Mutant Information

Mutant Name	FN2138-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN2138-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: 43

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 21827408 A-G Hetero INTERGENIC
SBS Chr1 22050540 G-A Hetero INTERGENIC
SBS Chr1 28980214 C-T Hetero INTERGENIC
SBS Chr2 13057489 C-T Hetero INTERGENIC
SBS Chr2 16910682 A-T Hetero INTERGENIC
SBS Chr2 18311234 T-C Hetero INTERGENIC
SBS Chr3 2564467 A-T Hetero INTERGENIC
SBS Chr3 16558624 G-A Hetero INTERGENIC
SBS Chr3 17900807 G-A Hetero INTERGENIC
SBS Chr3 20246999 C-G Hetero INTERGENIC
SBS Chr3 22965594 C-A Homo NON_SYNONYMOUS_CODING OsKitaake03g248300
SBS Chr3 22965596 G-A Homo SYNONYMOUS_CODING
SBS Chr5 4368437 C-A Hetero INTRON
SBS Chr5 12140317 G-A Hetero INTERGENIC
SBS Chr5 12374913 T-C Homo INTERGENIC
SBS Chr5 20016869 G-A Hetero INTERGENIC
SBS Chr5 21365278 C-T Hetero INTERGENIC
SBS Chr5 28856540 G-A Hetero INTERGENIC
SBS Chr6 8370269 C-A Hetero INTRON
SBS Chr6 9877527 C-T Hetero INTERGENIC
SBS Chr6 21765519 C-A Hetero INTERGENIC
SBS Chr6 24862992 G-A Hetero INTERGENIC
SBS Chr7 6610170 A-C Hetero INTERGENIC
SBS Chr7 7973261 G-A Hetero INTERGENIC
SBS Chr7 26971782 G-A Hetero INTERGENIC
SBS Chr7 28667353 G-A Homo INTRON
SBS Chr8 1920951 G-T Hetero INTERGENIC
SBS Chr8 3463875 G-A Hetero UTR_3_PRIME
SBS Chr8 6738251 A-G Hetero INTERGENIC
SBS Chr8 15404253 A-T Homo INTERGENIC
SBS Chr8 18397002 A-C Homo NON_SYNONYMOUS_CODING OsKitaake08g136900
SBS Chr8 18397003 C-T Homo SYNONYMOUS_CODING
SBS Chr8 26067539 A-G Hetero INTERGENIC
SBS Chr9 9884152 C-T Hetero INTERGENIC
SBS Chr9 10560447 T-G Hetero INTERGENIC
SBS Chr9 16575791 T-A Hetero INTERGENIC
SBS Chr10 6225250 A-G Hetero INTERGENIC
SBS Chr10 22477867 T-A Hetero INTERGENIC
SBS Chr10 22477868 A-T Hetero INTERGENIC
SBS Chr11 5365555 C-A Homo INTERGENIC
SBS Chr11 24442351 C-G Hetero INTERGENIC
SBS Chr12 12011121 T-C Homo INTRON
SBS Chr12 18822975 G-A Hetero INTERGENIC

Deletions: 17

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr3 343120 343123 3
Deletion Chr10 1588309 1588310 1
Deletion Chr10 1970001 1983000 12999 2
Deletion Chr3 2262516 2262517 1
Deletion Chr1 10593353 10593354 1
Deletion Chr6 16356637 16356639 2
Deletion Chr5 16861882 16861883 1
Deletion Chr3 17513001 17607000 93999 6
Deletion Chr11 18934231 18934232 1 OsKitaake11g147600
Deletion Chr2 19159032 19159048 16
Deletion Chr9 20116725 20116727 2
Deletion Chr9 20391522 20391529 7 OsKitaake09g171600
Deletion Chr8 23912261 23912272 11
Deletion Chr1 23944171 23944172 1
Deletion Chr11 25724043 25724044 1
Deletion Chr11 27124696 27124697 1
Deletion Chr1 42719001 42761000 41999 OsKitaake01g471100

Insertions: 7

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr2 14625215 14625219 3
Insertion Chr5 22809292 22809300 7
Insertion Chr7 4716952 4716955 2
Insertion Chr8 24862318 24862321 2
Insertion Chr10 9881998 9882001 2
Insertion Chr12 10016519 10016522 2
Insertion Chr12 25755958 25755961 2

Inversions: 7

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Inversion Chr2 13718662 13719527
Inversion Chr2 13718680 13719566
Inversion Chr3 17603378 17967811
Inversion Chr3 17748373 17967802
Inversion Chr7 26970601 26973133 OsKitaake07g251600
Inversion Chr7 26970603 26973139 OsKitaake07g251600
Inversion Chr1 42451244 42715680 2

Translocations: 5

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes

Translocation Chr8 15898464 Chr2 17410058
Translocation Chr8 15900025 Chr3 15341586
Translocation Chr8 15900311 Chr3 15341581
Translocation Chr12 24467834 Chr8 15899978
Translocation Chr12 24467837 Chr8 15898479

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	21827408	A-G	Hetero	INTERGENIC
SBS	Chr1	22050540	G-A	Hetero	INTERGENIC
SBS	Chr1	28980214	C-T	Hetero	INTERGENIC
SBS	Chr2	13057489	C-T	Hetero	INTERGENIC
SBS	Chr2	16910682	A-T	Hetero	INTERGENIC
SBS	Chr2	18311234	T-C	Hetero	INTERGENIC
SBS	Chr3	2564467	A-T	Hetero	INTERGENIC
SBS	Chr3	16558624	G-A	Hetero	INTERGENIC
SBS	Chr3	17900807	G-A	Hetero	INTERGENIC
SBS	Chr3	20246999	C-G	Hetero	INTERGENIC
SBS	Chr3	22965594	C-A	Homo	NON_SYNONYMOUS_CODING	OsKitaake03g248300
SBS	Chr3	22965596	G-A	Homo	SYNONYMOUS_CODING
SBS	Chr5	4368437	C-A	Hetero	INTRON
SBS	Chr5	12140317	G-A	Hetero	INTERGENIC
SBS	Chr5	12374913	T-C	Homo	INTERGENIC
SBS	Chr5	20016869	G-A	Hetero	INTERGENIC
SBS	Chr5	21365278	C-T	Hetero	INTERGENIC
SBS	Chr5	28856540	G-A	Hetero	INTERGENIC
SBS	Chr6	8370269	C-A	Hetero	INTRON
SBS	Chr6	9877527	C-T	Hetero	INTERGENIC
SBS	Chr6	21765519	C-A	Hetero	INTERGENIC
SBS	Chr6	24862992	G-A	Hetero	INTERGENIC
SBS	Chr7	6610170	A-C	Hetero	INTERGENIC
SBS	Chr7	7973261	G-A	Hetero	INTERGENIC
SBS	Chr7	26971782	G-A	Hetero	INTERGENIC
SBS	Chr7	28667353	G-A	Homo	INTRON
SBS	Chr8	1920951	G-T	Hetero	INTERGENIC
SBS	Chr8	3463875	G-A	Hetero	UTR_3_PRIME
SBS	Chr8	6738251	A-G	Hetero	INTERGENIC
SBS	Chr8	15404253	A-T	Homo	INTERGENIC
SBS	Chr8	18397002	A-C	Homo	NON_SYNONYMOUS_CODING	OsKitaake08g136900
SBS	Chr8	18397003	C-T	Homo	SYNONYMOUS_CODING
SBS	Chr8	26067539	A-G	Hetero	INTERGENIC
SBS	Chr9	9884152	C-T	Hetero	INTERGENIC
SBS	Chr9	10560447	T-G	Hetero	INTERGENIC
SBS	Chr9	16575791	T-A	Hetero	INTERGENIC
SBS	Chr10	6225250	A-G	Hetero	INTERGENIC
SBS	Chr10	22477867	T-A	Hetero	INTERGENIC
SBS	Chr10	22477868	A-T	Hetero	INTERGENIC
SBS	Chr11	5365555	C-A	Homo	INTERGENIC
SBS	Chr11	24442351	C-G	Hetero	INTERGENIC
SBS	Chr12	12011121	T-C	Homo	INTRON
SBS	Chr12	18822975	G-A	Hetero	INTERGENIC

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr3	343120	343123	3
Deletion	Chr10	1588309	1588310	1
Deletion	Chr10	1970001	1983000	12999	2
Deletion	Chr3	2262516	2262517	1
Deletion	Chr1	10593353	10593354	1
Deletion	Chr6	16356637	16356639	2
Deletion	Chr5	16861882	16861883	1
Deletion	Chr3	17513001	17607000	93999	6
Deletion	Chr11	18934231	18934232	1	OsKitaake11g147600
Deletion	Chr2	19159032	19159048	16
Deletion	Chr9	20116725	20116727	2
Deletion	Chr9	20391522	20391529	7	OsKitaake09g171600
Deletion	Chr8	23912261	23912272	11
Deletion	Chr1	23944171	23944172	1
Deletion	Chr11	25724043	25724044	1
Deletion	Chr11	27124696	27124697	1
Deletion	Chr1	42719001	42761000	41999	OsKitaake01g471100

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr2	13718662	13719527
Inversion	Chr2	13718680	13719566
Inversion	Chr3	17603378	17967811
Inversion	Chr3	17748373	17967802
Inversion	Chr7	26970601	26973133	OsKitaake07g251600
Inversion	Chr7	26970603	26973139	OsKitaake07g251600
Inversion	Chr1	42451244	42715680	2

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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