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Detailed information for vg0901473638:

Variant ID: vg0901473638 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 1473638
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.03, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:

AAATGCCGATGACATATCATTTATCTTTGAGCTAATGTCATCTGTGTATCGATCGGCAGTCATGAATAAGTAAAGAAGAACTAAATCTACTCGATCGGCT[G/A]
TAGATATTAATGATATATACTCCTTATATCGATGTATACTTAAATCAAGTGATTGGGATAGATCGGTCATCATGCCGAGACAGTATAAATCACTTTGATC

Reverse complement sequence

GATCAAAGTGATTTATACTGTCTCGGCATGATGACCGATCTATCCCAATCACTTGATTTAAGTATACATCGATATAAGGAGTATATATCATTAATATCTA[C/T]
AGCCGATCGAGTAGATTTAGTTCTTCTTTACTTATTCATGACTGCCGATCGATACACAGATGACATTAGCTCAAAGATAAATGATATGTCATCGGCATTT

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	53.90%	45.90%	0.17%	0.00%	NA
All Indica	2759	88.60%	11.30%	0.07%	0.00%	NA
All Japonica	1512	1.10%	98.90%	0.00%	0.00%	NA
Aus	269	17.80%	82.20%	0.00%	0.00%	NA
Indica I	595	93.80%	6.20%	0.00%	0.00%	NA
Indica II	465	84.70%	15.30%	0.00%	0.00%	NA
Indica III	913	92.40%	7.40%	0.11%	0.00%	NA
Indica Intermediate	786	82.40%	17.40%	0.13%	0.00%	NA
Temperate Japonica	767	0.80%	99.20%	0.00%	0.00%	NA
Tropical Japonica	504	1.00%	99.00%	0.00%	0.00%	NA
Japonica Intermediate	241	2.10%	97.90%	0.00%	0.00%	NA
VI/Aromatic	96	4.20%	94.80%	1.04%	0.00%	NA
Intermediate	90	40.00%	54.40%	5.56%	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
vg0901473638	G -> A	LOC_Os09g03090.1	upstream_gene_variant ; 3195.0bp to feature; MODIFIER	silent_mutation	Average:36.51; most accessible tissue: Zhenshan97 flag leaf, score: 60.074	N	N	N	N
vg0901473638	G -> A	LOC_Os09g03100.1	upstream_gene_variant ; 1503.0bp to feature; MODIFIER	silent_mutation	Average:36.51; most accessible tissue: Zhenshan97 flag leaf, score: 60.074	N	N	N	N
vg0901473638	G -> A	LOC_Os09g03090-LOC_Os09g03100	intergenic_region ; MODIFIER	silent_mutation	Average:36.51; most accessible tissue: Zhenshan97 flag leaf, score: 60.074	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0901473638	5.41E-07	5.41E-07	mr1445	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
vg0901473638	NA	2.08E-11	mr1781_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