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Detailed information for vg0326593742:

Variant ID: vg0326593742 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 26593742
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: 124. )

Flanking Sequence (100 bp) in Reference Genome:

ATGATTTTGTTGTGGATGATTTGTGGGGATTTGGGGTGAAAATTAATTGATGGATGCAGTACAAAACAATGAAAGAAAAAGAAAAAAATTAGTAGCAACC[G/A]
GGAGTAAAGATGGTAGCGCCACCTGGCGCTACCATCTTTAGTCCCGGTTGATGTTACACCTGGCCTAGAGGGGGTCTAGGCATCTTTAGATGGGTATCTT

Reverse complement sequence

AAGATACCCATCTAAAGATGCCTAGACCCCCTCTAGGCCAGGTGTAACATCAACCGGGACTAAAGATGGTAGCGCCAGGTGGCGCTACCATCTTTACTCC[C/T]
GGTTGCTACTAATTTTTTTCTTTTTCTTTCATTGTTTTGTACTGCATCCATCAATTAATTTTCACCCCAAATCCCCACAAATCATCCACAACAAAATCAT

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	96.80%	2.20%	0.97%	0.00%	NA
All Indica	2759	99.30%	0.10%	0.51%	0.00%	NA
All Japonica	1512	91.80%	6.30%	1.92%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.00%	0.00%	2.02%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.40%	0.40%	0.25%	0.00%	NA
Temperate Japonica	767	99.60%	0.00%	0.39%	0.00%	NA
Tropical Japonica	504	78.40%	17.50%	4.17%	0.00%	NA
Japonica Intermediate	241	95.00%	2.90%	2.07%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	93.30%	4.40%	2.22%	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
vg0326593742	G -> A	LOC_Os03g47030.1	downstream_gene_variant ; 1840.0bp to feature; MODIFIER	silent_mutation	Average:44.485; most accessible tissue: Callus, score: 69.337	N	N	N	N
vg0326593742	G -> A	LOC_Os03g47030-LOC_Os03g47034	intergenic_region ; MODIFIER	silent_mutation	Average:44.485; most accessible tissue: Callus, score: 69.337	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0326593742	NA	8.97E-06	mr1188	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
vg0326593742	NA	1.85E-08	mr1188_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
vg0326593742	7.86E-06	6.91E-08	mr1217_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