Search for Variation information by Variation ID:

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

Detailed information for vg0329646866:

Variant ID: vg0329646866 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 29646866
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, T: 0.01, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

GGAAAGGTTTTTGGGAAGCGCTTTGCGCGACTGCTCCCTGTTCGTCCGCGATGGCTCGCCTTCCTCTCCGCTCGCGTGCTGCGCGCCTTCGTCGACGCCC[G/A]
CAACCGCGAGTAGTTCCTGCCGAGCAACCGGTCTTTCCGCCACCTCGGTACGTGTTCGATATGTTACGCATATTTGATCTGTTCATGTTTTACTACTTAG

Reverse complement sequence

CTAAGTAGTAAAACATGAACAGATCAAATATGCGTAACATATCGAACACGTACCGAGGTGGCGGAAAGACCGGTTGCTCGGCAGGAACTACTCGCGGTTG[C/T]
GGGCGTCGACGAAGGCGCGCAGCACGCGAGCGGAGAGGAAGGCGAGCCATCGCGGACGAACAGGGAGCAGTCGCGCAAAGCGCTTCCCAAAAACCTTTCC

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	85.80%	14.20%	0.06%	0.00%	NA
All Indica	2759	76.20%	23.70%	0.07%	0.00%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	70.30%	29.60%	0.17%	0.00%	NA
Indica II	465	66.00%	34.00%	0.00%	0.00%	NA
Indica III	913	81.40%	18.50%	0.11%	0.00%	NA
Indica Intermediate	786	80.80%	19.20%	0.00%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	88.90%	10.00%	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
vg0329646866	G -> A	LOC_Os03g51724.1	synonymous_variant ; p.Pro17Pro; LOW	synonymous_codon	Average:36.35; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0329646866	3.23E-06	1.04E-06	mr1786	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