Search Nipponbare

Mutant Information

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

Mutant Name	FN1315-S [Download]
Generation	M2-SOS
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN1315-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
Mapping (Hover to Zoom-In)

Variant Information

Single base substitutions: 34

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	21079068	C-A	HOMO	INTRON
SBS	Chr1	27468775	C-A	HET	INTERGENIC
SBS	Chr10	13689200	C-T	HOMO	INTERGENIC
SBS	Chr10	15510893	G-A	HOMO	INTERGENIC
SBS	Chr10	20872318	A-G	HET	INTRON
SBS	Chr11	21000810	C-T	HET	INTERGENIC
SBS	Chr11	21007908	C-A	HET	INTERGENIC
SBS	Chr11	7391556	G-T	HET	INTERGENIC
SBS	Chr2	13138667	C-T	HET	INTRON
SBS	Chr2	15424698	G-T	HET	INTERGENIC
SBS	Chr2	17576388	G-C	HET	UTR_5_PRIME
SBS	Chr3	15972248	C-A	HET	INTERGENIC
SBS	Chr3	22251344	T-A	HET	INTERGENIC
SBS	Chr3	22843833	C-A	HET	INTERGENIC
SBS	Chr3	33122697	C-T	HOMO	INTERGENIC
SBS	Chr4	19594722	G-A	HOMO	SYNONYMOUS_CODING
SBS	Chr4	20080023	C-T	HOMO	INTRON
SBS	Chr4	23674212	T-G	HET	INTERGENIC
SBS	Chr4	26022096	C-T	HET	INTERGENIC
SBS	Chr4	26826213	A-G	HET	INTERGENIC
SBS	Chr4	5374907	C-T	HET	INTERGENIC
SBS	Chr5	22689132	C-T	HOMO	INTERGENIC
SBS	Chr5	27530780	G-A	HOMO	SYNONYMOUS_CODING
SBS	Chr5	28787980	G-A	HOMO	NON_SYNONYMOUS_CODING	LOC_Os05g50230
SBS	Chr5	6720174	T-C	HET	INTERGENIC
SBS	Chr6	16005065	G-T	HET	STOP_GAINED	LOC_Os06g28170
SBS	Chr6	21598690	T-A	HET	NON_SYNONYMOUS_CODING	LOC_Os06g36700
SBS	Chr6	21598691	T-A	HET	SYNONYMOUS_CODING
SBS	Chr6	25204418	C-T	HET	INTRON
SBS	Chr7	10608673	C-T	HOMO	INTERGENIC
SBS	Chr7	16065069	G-A	HET	INTERGENIC
SBS	Chr7	6454902	G-T	HOMO	INTRON
SBS	Chr7	9605013	C-A	HET	INTERGENIC
SBS	Chr8	10670771	T-A	HOMO	INTERGENIC

Deletions: 24

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Deletion	Chr7	189791	189794	3
Deletion	Chr1	965100	965116	16	LOC_Os01g02770
Deletion	Chr1	3343001	3513000	170000	30
Deletion	Chr4	6759183	6759187	4	LOC_Os04g12240
Deletion	Chr5	6800001	6918000	118000	14
Deletion	Chr10	8572433	8572440	7
Deletion	Chr3	8714778	8714779	1
Deletion	Chr12	9122748	9122750	2
Deletion	Chr11	9745003	9745006	3
Deletion	Chr5	12262840	12262843	3
Deletion	Chr9	12687432	12687436	4
Deletion	Chr9	13524652	13524655	3
Deletion	Chr6	16330445	16330464	19	LOC_Os06g28670
Deletion	Chr10	17515418	17522179	6761	LOC_Os10g33330
Deletion	Chr10	18811910	18811918	8	LOC_Os10g35210
Deletion	Chr10	18899571	18899572	1
Deletion	Chr2	19532835	19532843	8	LOC_Os02g32880
Deletion	Chr7	20478042	20478044	2	LOC_Os07g34220
Deletion	Chr4	21092755	21092756	1
Deletion	Chr4	21145753	21145759	6
Deletion	Chr5	21312869	21312906	37
Deletion	Chr9	21313001	21345000	32000	9
Deletion	Chr12	24122188	24122197	9
Deletion	Chr2	25438056	25438065	9	LOC_Os02g42300

Insertions: 4

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Insertion	Chr4	4124944	4125002	59	LOC_Os04g07760
Insertion	Chr8	22263271	22263271	1
Insertion	Chr8	23997676	23997676	1
Insertion	Chr9	10754979	10754979	1

Inversions: 3

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr1	3343015	3657341
Inversion	Chr1	3513011	3657342	LOC_Os01g07410
Inversion	Chr6	15881095	16404416	LOC_Os06g28820

Translocations: 3

Variant Type	Chromosome	Position 1	Chromosome	Position 2	Number of Genes
Translocation	Chr6	16404465	Chr2	35924225	2
Translocation	Chr11	16639139	Chr6	16423793	2
Translocation	Chr11	16639168	Chr6	16404416	2

Main menu