Search for Variation information by Variation ID:

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

Detailed information for vg0703625452:

Variant ID: vg0703625452 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 3625452
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: 263. )

Flanking Sequence (100 bp) in Reference Genome:

CCATTAAAACATTTTTTCTTGAAATACTTGTTGAAACATATGTTTTCCTTTCATTAGAATATAATCATGCAATATCTTATTGTAATGATTTAATTGCAAC[G/A]
AATACAATGATGTGGTTGGATGGTAGACCAGATAAGTAATCCAAGAGAAGAAATATTTTAAGCTTACTAATAAATTAAGCCTTATATGCATGCAAGAGTA

Reverse complement sequence

TACTCTTGCATGCATATAAGGCTTAATTTATTAGTAAGCTTAAAATATTTCTTCTCTTGGATTACTTATCTGGTCTACCATCCAACCACATCATTGTATT[C/T]
GTTGCAATTAAATCATTACAATAAGATATTGCATGATTATATTCTAATGAAAGGAAAACATATGTTTCAACAAGTATTTCAAGAAAAAATGTTTTAATGG

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	91.90%	7.10%	0.99%	0.00%	NA
All Indica	2759	99.80%	0.10%	0.07%	0.00%	NA
All Japonica	1512	80.60%	16.50%	2.91%	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	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.40%	0.40%	0.25%	0.00%	NA
Temperate Japonica	767	83.60%	12.80%	3.65%	0.00%	NA
Tropical Japonica	504	73.80%	24.60%	1.59%	0.00%	NA
Japonica Intermediate	241	85.10%	11.60%	3.32%	0.00%	NA
VI/Aromatic	96	24.00%	76.00%	0.00%	0.00%	NA
Intermediate	90	87.80%	11.10%	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
vg0703625452	G -> A	LOC_Os07g07300.1	intron_variant ; MODIFIER	silent_mutation	Average:37.287; most accessible tissue: Callus, score: 72.006	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0703625452	3.58E-07	NA	mr1631_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
vg0703625452	NA	3.66E-06	mr1631_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
vg0703625452	NA	1.01E-09	mr1829_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