Search for Variation information by Variation ID:

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

Detailed information for vg0629714028:

Variant ID: vg0629714028 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 29714028
Reference Allele: C	Alternative Allele: G
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, G: 0.08, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

GATATCATCGTTCATGCTGGGGAGCTAGTTCCTATGCCCATATCGAGCTATCTATGTCATGGGCAACTTAAGGGATTTTCAACCTGGAAGCATGCTTTGC[C/G]
TTGCTATGCAGTAATCCCTGATAGGCAAAACCTCAAAAGCAGCCAAGAAGCTGAATCACTAGAACGTGCCATCAGAATAGTTCAAACTTCAAATGCAACA

Reverse complement sequence

TGTTGCATTTGAAGTTTGAACTATTCTGATGGCACGTTCTAGTGATTCAGCTTCTTGGCTGCTTTTGAGGTTTTGCCTATCAGGGATTACTGCATAGCAA[G/C]
GCAAAGCATGCTTCCAGGTTGAAAATCCCTTAAGTTGCCCATGACATAGATAGCTCGATATGGGCATAGGAACTAGCTCCCCAGCATGAACGATGATATC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	56.20%	43.70%	0.15%	0.00%	NA
All Indica	2759	90.80%	9.00%	0.18%	0.00%	NA
All Japonica	1512	2.60%	97.40%	0.07%	0.00%	NA
Aus	269	22.30%	77.70%	0.00%	0.00%	NA
Indica I	595	89.20%	10.40%	0.34%	0.00%	NA
Indica II	465	90.50%	9.20%	0.22%	0.00%	NA
Indica III	913	94.00%	6.00%	0.00%	0.00%	NA
Indica Intermediate	786	88.40%	11.30%	0.25%	0.00%	NA
Temperate Japonica	767	3.50%	96.30%	0.13%	0.00%	NA
Tropical Japonica	504	1.00%	99.00%	0.00%	0.00%	NA
Japonica Intermediate	241	2.90%	97.10%	0.00%	0.00%	NA
VI/Aromatic	96	3.10%	95.80%	1.04%	0.00%	NA
Intermediate	90	52.20%	47.80%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0629714028	C -> G	LOC_Os06g49020.1	upstream_gene_variant ; 1313.0bp to feature; MODIFIER	silent_mutation	Average:64.096; most accessible tissue: Callus, score: 88.277	N	N	N	N
vg0629714028	C -> G	LOC_Os06g49030.1	intron_variant ; MODIFIER	silent_mutation	Average:64.096; most accessible tissue: Callus, score: 88.277	N	N	N	N
vg0629714028	C -> G	LOC_Os06g49030.2	intron_variant ; MODIFIER	silent_mutation	Average:64.096; most accessible tissue: Callus, score: 88.277	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0629714028	NA	1.43E-22	mr1003	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
vg0629714028	NA	4.76E-23	mr1051	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
vg0629714028	NA	4.32E-11	mr1657	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
vg0629714028	NA	4.90E-28	mr1051_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