Search for Variation information by Variation ID:

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

Detailed information for vg0141000513:

Variant ID: vg0141000513 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 41000513
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, G: 0.00, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:

AAATAGAAGCATTAGTAGTTAAATAAATGTTCAGAAATTAGAGCGAGTAATAAGGCAAAGTTTTTGCCTTTGTTCTAAAAAAAACTTTGCTGACTACCTC[C/G]
CTGACGATTCCCATGTGCTTGCCGACGCATGGCATGGACGAGGCGGCAAACACGGCCACGGCGATCTTGTCCGGGAACCTCTCCATTGCGAGCGCGATGC

Reverse complement sequence

GCATCGCGCTCGCAATGGAGAGGTTCCCGGACAAGATCGCCGTGGCCGTGTTTGCCGCCTCGTCCATGCCATGCGTCGGCAAGCACATGGGAATCGTCAG[G/C]
GAGGTAGTCAGCAAAGTTTTTTTTAGAACAAAGGCAAAAACTTTGCCTTATTACTCGCTCTAATTTCTGAACATTTATTTAACTACTAATGCTTCTATTT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	69.80%	29.60%	0.11%	0.53%	NA
All Indica	2759	50.10%	48.90%	0.18%	0.83%	NA
All Japonica	1512	99.00%	1.00%	0.00%	0.00%	NA
Aus	269	95.50%	4.10%	0.00%	0.37%	NA
Indica I	595	56.00%	43.40%	0.34%	0.34%	NA
Indica II	465	24.90%	74.40%	0.00%	0.65%	NA
Indica III	913	55.20%	43.70%	0.11%	0.99%	NA
Indica Intermediate	786	54.50%	44.10%	0.25%	1.15%	NA
Temperate Japonica	767	99.50%	0.50%	0.00%	0.00%	NA
Tropical Japonica	504	98.40%	1.60%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	73.30%	25.60%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0141000513	C -> G	LOC_Os01g70830.1	missense_variant ; p.Arg102Ser; MODERATE	nonsynonymous_codon ; R102S	Average:71.345; most accessible tissue: Callus, score: 82.749	benign	0.843	TOLERATED	0.72
vg0141000513	C -> DEL	LOC_Os01g70830.1	N	frameshift_variant	Average:71.345; most accessible tissue: Callus, score: 82.749	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0141000513	NA	9.41E-11	mr1457	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
vg0141000513	4.79E-06	NA	mr1458	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