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Detailed information for vg0628633192:

Variant ID: vg0628633192 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 28633192
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.61, G: 0.39, others allele: 0.00, population size: 41. )

Flanking Sequence (100 bp) in Reference Genome:

TGAGTTACGACTACTACCCGGTTCTTGACCAGAGGTGTAGCGATTCTCCCATTACCTCTACTTCAACAAGTGTTTTACCCAGAGATCCCTTACCACAAAG[A/G]
CACCTAGTGTTGAAACCTTTCCTAATGTCCTTTTACGCCATCTTGACAAAGCCTCTGAGGAACCTAAGGGAACTTCGGCTGGGGACGCCCAGAGCGGATA

Reverse complement sequence

TATCCGCTCTGGGCGTCCCCAGCCGAAGTTCCCTTAGGTTCCTCAGAGGCTTTGTCAAGATGGCGTAAAAGGACATTAGGAAAGGTTTCAACACTAGGTG[T/C]
CTTTGTGGTAAGGGATCTCTGGGTAAAACACTTGTTGAAGTAGAGGTAATGGGAGAATCGCTACACCTCTGGTCAAGAACCGGGTAGTAGTCGTAACTCA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	59.50%	40.50%	0.04%	0.00%	NA
All Indica	2759	39.90%	60.10%	0.07%	0.00%	NA
All Japonica	1512	98.30%	1.70%	0.00%	0.00%	NA
Aus	269	34.20%	65.80%	0.00%	0.00%	NA
Indica I	595	58.70%	41.20%	0.17%	0.00%	NA
Indica II	465	14.40%	85.60%	0.00%	0.00%	NA
Indica III	913	40.40%	59.50%	0.11%	0.00%	NA
Indica Intermediate	786	40.10%	59.90%	0.00%	0.00%	NA
Temperate Japonica	767	97.30%	2.70%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	86.50%	13.50%	0.00%	0.00%	NA
Intermediate	90	54.40%	45.60%	0.00%	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
vg0628633192	A -> G	LOC_Os06g47220.1	upstream_gene_variant ; 3283.0bp to feature; MODIFIER	silent_mutation	Average:39.807; most accessible tissue: Minghui63 young leaf, score: 54.11	N	N	N	N
vg0628633192	A -> G	LOC_Os06g47220-LOC_Os06g47230	intergenic_region ; MODIFIER	silent_mutation	Average:39.807; most accessible tissue: Minghui63 young leaf, score: 54.11	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0628633192	NA	7.30E-09	mr1974_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
vg0628633192	8.03E-06	2.56E-08	mr1974_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