Search for Variation information by Variation ID:

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

Detailed information for vg0306976273:

Variant ID: vg0306976273 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 6976273
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:

AGAATGCTAAGAAATGAAATTTGCTGAAAGTGTCAGTGCAAAAGAATACAAGATTCATTCTCATTTGGTCTGAATTCATCCATCGAAAACGCCATTATAA[G/A]
CATTAAGTAATCTCATGATTCTAAACTACTTGTATGTCTCCCAGAAACAAACTTGTACTTGTAATGCATGTGGAGTATTTGTTATTTCATCACAATTTTT

Reverse complement sequence

AAAAATTGTGATGAAATAACAAATACTCCACATGCATTACAAGTACAAGTTTGTTTCTGGGAGACATACAAGTAGTTTAGAATCATGAGATTACTTAATG[C/T]
TTATAATGGCGTTTTCGATGGATGAATTCAGACCAAATGAGAATGAATCTTGTATTCTTTTGCACTGACACTTTCAGCAAATTTCATTTCTTAGCATTCT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	95.80%	3.70%	0.49%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.04%	0.00%	NA
All Japonica	1512	87.10%	11.50%	1.39%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.00%	0.13%	0.00%	NA
Temperate Japonica	767	98.30%	0.10%	1.56%	0.00%	NA
Tropical Japonica	504	64.70%	33.90%	1.39%	0.00%	NA
Japonica Intermediate	241	98.30%	0.80%	0.83%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	2.20%	1.11%	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
vg0306976273	G -> A	LOC_Os03g12940.1	downstream_gene_variant ; 4366.0bp to feature; MODIFIER	silent_mutation	Average:47.436; most accessible tissue: Callus, score: 86.598	N	N	N	N
vg0306976273	G -> A	LOC_Os03g12940.2	downstream_gene_variant ; 4369.0bp to feature; MODIFIER	silent_mutation	Average:47.436; most accessible tissue: Callus, score: 86.598	N	N	N	N
vg0306976273	G -> A	LOC_Os03g12930.1	intron_variant ; MODIFIER	silent_mutation	Average:47.436; most accessible tissue: Callus, score: 86.598	N	N	N	N
vg0306976273	G -> A	LOC_Os03g12930.2	intron_variant ; MODIFIER	silent_mutation	Average:47.436; most accessible tissue: Callus, score: 86.598	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0306976273	NA	1.74E-06	mr1063_2	Jap_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
vg0306976273	NA	2.00E-06	mr1072_2	Jap_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
vg0306976273	NA	6.24E-06	mr1075_2	Jap_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
vg0306976273	NA	5.06E-06	mr1077_2	Jap_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
vg0306976273	NA	7.53E-06	mr1200_2	Jap_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
vg0306976273	NA	2.91E-07	mr1220_2	Jap_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
vg0306976273	NA	9.78E-06	mr1252_2	Jap_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
vg0306976273	NA	5.52E-06	mr1295_2	Jap_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
vg0306976273	NA	1.17E-06	mr1739_2	Jap_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