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Detailed information for vg0528917046:

Variant ID: vg0528917046 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 28917046
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: 318. )

Flanking Sequence (100 bp) in Reference Genome:

TGCACCTTCTGTTCTCTACAGGCTATTAGTTGCTCAGGTGAACCATGCTATTGAGGCTGAAGGAATTATCAGCACGGAATGATCGGTGGTGGGAACGTGT[G/A]
TTTGGGGTAGGCGGTAGATGAGGGAGAAATAAGTTCTCTATACTGATTAATGCAAACCATGGTTTAGTAAGATTTCAAGAGGCTTGACTACTTGATCATG

Reverse complement sequence

CATGATCAAGTAGTCAAGCCTCTTGAAATCTTACTAAACCATGGTTTGCATTAATCAGTATAGAGAACTTATTTCTCCCTCATCTACCGCCTACCCCAAA[C/T]
ACACGTTCCCACCACCGATCATTCCGTGCTGATAATTCCTTCAGCCTCAATAGCATGGTTCACCTGAGCAACTAATAGCCTGTAGAGAACAGAAGGTGCA

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	96.00%	3.50%	0.51%	0.00%	NA
All Indica	2759	95.50%	4.20%	0.33%	0.00%	NA
All Japonica	1512	95.90%	3.20%	0.93%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.20%	0.80%	0.00%	0.00%	NA
Indica II	465	82.40%	15.90%	1.72%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	95.40%	4.50%	0.13%	0.00%	NA
Temperate Japonica	767	99.30%	0.30%	0.39%	0.00%	NA
Tropical Japonica	504	89.90%	7.90%	2.18%	0.00%	NA
Japonica Intermediate	241	97.50%	2.50%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	3.30%	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
vg0528917046	G -> A	LOC_Os05g50420.1	upstream_gene_variant ; 4851.0bp to feature; MODIFIER	silent_mutation	Average:67.916; most accessible tissue: Zhenshan97 flower, score: 81.724	N	N	N	N
vg0528917046	G -> A	LOC_Os05g50450.1	downstream_gene_variant ; 2922.0bp to feature; MODIFIER	silent_mutation	Average:67.916; most accessible tissue: Zhenshan97 flower, score: 81.724	N	N	N	N
vg0528917046	G -> A	LOC_Os05g50440.1	intron_variant ; MODIFIER	silent_mutation	Average:67.916; most accessible tissue: Zhenshan97 flower, score: 81.724	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0528917046	NA	6.67E-06	mr1332_2	Ind_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
vg0528917046	NA	1.99E-06	mr1478_2	Ind_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
vg0528917046	NA	8.46E-07	mr1588_2	Ind_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
vg0528917046	NA	1.80E-08	mr1828_2	Ind_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
vg0528917046	3.00E-06	NA	mr1932_2	Ind_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