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Detailed information for vg0334067609:

Variant ID: vg0334067609 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 34067609
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.04, others allele: 0.00, population size: 28. )

Flanking Sequence (100 bp) in Reference Genome:

AGGGTGAGTGTGGTGTTGCGTGTGTAGTGGTGTGCGTGCGTGTTCATCAGATGTCTAATTAAAAAAATATTGAAGTTATCACAAAACTAAATACTGTAGA[G/A]
TTTATCTCCAACACTACCGTTATGTTTGAGCTATAAATATAGTAGTGTTGTGATTAAATTAGCACTAAACCTATAGTTTGTGATAAATTTATCATCTAGT

Reverse complement sequence

ACTAGATGATAAATTTATCACAAACTATAGGTTTAGTGCTAATTTAATCACAACACTACTATATTTATAGCTCAAACATAACGGTAGTGTTGGAGATAAA[C/T]
TCTACAGTATTTAGTTTTGTGATAACTTCAATATTTTTTTAATTAGACATCTGATGAACACGCACGCACACCACTACACACGCAACACCACACTCACCCT

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	53.10%	45.20%	0.72%	1.04%	NA
All Indica	2759	32.90%	66.20%	0.91%	0.00%	NA
All Japonica	1512	99.10%	0.60%	0.07%	0.20%	NA
Aus	269	3.70%	95.50%	0.74%	0.00%	NA
Indica I	595	55.60%	43.40%	1.01%	0.00%	NA
Indica II	465	14.80%	83.20%	1.94%	0.00%	NA
Indica III	913	33.00%	66.60%	0.44%	0.00%	NA
Indica Intermediate	786	26.30%	72.90%	0.76%	0.00%	NA
Temperate Japonica	767	99.60%	0.30%	0.13%	0.00%	NA
Tropical Japonica	504	98.60%	1.40%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	0.00%	0.00%	1.24%	NA
VI/Aromatic	96	44.80%	8.30%	2.08%	44.79%	NA
Intermediate	90	54.40%	37.80%	4.44%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0334067609	G -> A	LOC_Os03g59830.1	upstream_gene_variant ; 1506.0bp to feature; MODIFIER	silent_mutation	Average:22.693; most accessible tissue: Callus, score: 44.943	N	N	N	N
vg0334067609	G -> A	LOC_Os03g59840.1	downstream_gene_variant ; 2813.0bp to feature; MODIFIER	silent_mutation	Average:22.693; most accessible tissue: Callus, score: 44.943	N	N	N	N
vg0334067609	G -> A	LOC_Os03g59820-LOC_Os03g59830	intergenic_region ; MODIFIER	silent_mutation	Average:22.693; most accessible tissue: Callus, score: 44.943	N	N	N	N
vg0334067609	G -> DEL	N	N	silent_mutation	Average:22.693; most accessible tissue: Callus, score: 44.943	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0334067609	NA	3.32E-06	mr1424	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
vg0334067609	4.86E-06	4.85E-06	mr1885	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