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Detailed information for vg0516498972:

Variant ID: vg0516498972 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 16498972
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.79, A: 0.21, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

TTTGAGGAGAGGAGATAGAGAAGATCGGGAAGACACGCAAAACAAGATGAGTCATTATCACATGATTAATTGACTATTAACTATTTTAAATTTTAAAAAT[G/A]
AATTAATATAATTTTTAAAGCAACTTTCCTATAGAAATTTTTTGCAAGAAACACACCGTTTAGTAGTTTGGAAATCGTGCGCGTGGAAAACGAAACAAAC

Reverse complement sequence

GTTTGTTTCGTTTTCCACGCGCACGATTTCCAAACTACTAAACGGTGTGTTTCTTGCAAAAAATTTCTATAGGAAAGTTGCTTTAAAAATTATATTAATT[C/T]
ATTTTTAAAATTTAAAATAGTTAATAGTCAATTAATCATGTGATAATGACTCATCTTGTTTTGCGTGTCTTCCCGATCTTCTCTATCTCCTCTCCTCAAA

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	65.60%	34.10%	0.32%	0.00%	NA
All Indica	2759	72.30%	27.30%	0.40%	0.00%	NA
All Japonica	1512	45.80%	54.20%	0.07%	0.00%	NA
Aus	269	97.80%	2.20%	0.00%	0.00%	NA
Indica I	595	58.00%	41.20%	0.84%	0.00%	NA
Indica II	465	56.80%	42.60%	0.65%	0.00%	NA
Indica III	913	84.10%	15.90%	0.00%	0.00%	NA
Indica Intermediate	786	78.50%	21.10%	0.38%	0.00%	NA
Temperate Japonica	767	76.90%	23.10%	0.00%	0.00%	NA
Tropical Japonica	504	6.70%	93.30%	0.00%	0.00%	NA
Japonica Intermediate	241	28.20%	71.40%	0.41%	0.00%	NA
VI/Aromatic	96	91.70%	7.30%	1.04%	0.00%	NA
Intermediate	90	67.80%	30.00%	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
vg0516498972	G -> A	LOC_Os05g28190.1	downstream_gene_variant ; 3963.0bp to feature; MODIFIER	silent_mutation	Average:71.947; most accessible tissue: Zhenshan97 flower, score: 90.197	N	N	N	N
vg0516498972	G -> A	LOC_Os05g28180-LOC_Os05g28190	intergenic_region ; MODIFIER	silent_mutation	Average:71.947; most accessible tissue: Zhenshan97 flower, score: 90.197	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0516498972	NA	5.50E-06	mr1184_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
vg0516498972	1.61E-06	1.60E-06	mr1192_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
vg0516498972	NA	6.71E-07	mr1369_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
vg0516498972	NA	4.47E-06	mr1397_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
vg0516498972	NA	5.22E-07	mr1453_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
vg0516498972	NA	1.05E-09	mr1486_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
vg0516498972	NA	3.23E-08	mr1582_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
vg0516498972	NA	9.24E-06	mr1652_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