Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0114201104:

Variant ID: vg0114201104 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 14201104
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.81, T: 0.19, others allele: 0.00, population size: 85. )

Flanking Sequence (100 bp) in Reference Genome:

CTTTAAAAAATCTCTCCGTAACATGTTATTTTAGTAAAATGGAGGTTGTGGGAACAAATCTATTCACATATGTGTGTGCTATGATTTTTTTCTTCCTCAC[C/T]
AGAACAAATCTTGTAATAGATCTAACGATTCAAAATTACGTGAAACTAACATACAAGTTACACTATAGTTACATGCAAGTTACAATGTAATTACAAACAA

Reverse complement sequence

TTGTTTGTAATTACATTGTAACTTGCATGTAACTATAGTGTAACTTGTATGTTAGTTTCACGTAATTTTGAATCGTTAGATCTATTACAAGATTTGTTCT[G/A]
GTGAGGAAGAAAAAAATCATAGCACACACATATGTGAATAGATTTGTTCCCACAACCTCCATTTTACTAAAATAACATGTTACGGAGAGATTTTTTAAAG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	36.40%	31.20%	0.30%	32.10%	NA
All Indica	2759	6.10%	45.80%	0.43%	47.73%	NA
All Japonica	1512	95.40%	4.50%	0.00%	0.13%	NA
Aus	269	4.10%	32.30%	0.74%	62.83%	NA
Indica I	595	4.50%	41.70%	0.84%	52.94%	NA
Indica II	465	16.80%	13.30%	0.22%	69.68%	NA
Indica III	913	1.20%	66.90%	0.00%	31.87%	NA
Indica Intermediate	786	6.50%	43.50%	0.76%	49.24%	NA
Temperate Japonica	767	98.40%	1.60%	0.00%	0.00%	NA
Tropical Japonica	504	89.50%	10.30%	0.00%	0.20%	NA
Japonica Intermediate	241	97.90%	1.70%	0.00%	0.41%	NA
VI/Aromatic	96	53.10%	44.80%	0.00%	2.08%	NA
Intermediate	90	55.60%	14.40%	0.00%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0114201104	C -> T	LOC_Os01g25150-LOC_Os01g25160	intergenic_region ; MODIFIER	silent_mutation	Average:17.003; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg0114201104	C -> DEL	N	N	silent_mutation	Average:17.003; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0114201104	NA	1.38E-07	mr1030_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0114201104	3.41E-06	NA	mr1260_2	All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0114201104	NA	5.43E-06	mr1364_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0114201104	NA	1.59E-06	mr1555_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0114201104	NA	6.96E-13	mr1770_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251