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Detailed information for vg0118489802:

Variant ID: vg0118489802 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 18489802
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, others allele: 0.00, population size: 41. )

Flanking Sequence (100 bp) in Reference Genome:

CTCTCACCCATGCCTATATAAAGCATCCCCTAGTCATTCTATTCCGTTTGCCTCAAGTCCAAGCCGCGTGAGCCCTAGCGTCGCCGTCGCTGCTTCAGCC[G/A]
CGCCGCGCAACTGCTGTGGTCGTCGCTGTCACGTCCTGATAAATTCATCCCGAAATTAAAAATCATTTTCTAAAAGGAATAATAGAATTAATTAAAATTC

Reverse complement sequence

GAATTTTAATTAATTCTATTATTCCTTTTAGAAAATGATTTTTAATTTCGGGATGAATTTATCAGGACGTGACAGCGACGACCACAGCAGTTGCGCGGCG[C/T]
GGCTGAAGCAGCGACGGCGACGCTAGGGCTCACGCGGCTTGGACTTGAGGCAAACGGAATAGAATGACTAGGGGATGCTTTATATAGGCATGGGTGAGAG

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	39.30%	11.10%	6.41%	43.21%	NA
All Indica	2759	9.10%	17.90%	8.59%	64.41%	NA
All Japonica	1512	87.70%	0.20%	2.91%	9.19%	NA
Aus	269	52.80%	7.40%	5.20%	34.57%	NA
Indica I	595	2.70%	24.20%	6.89%	66.22%	NA
Indica II	465	12.00%	13.50%	4.52%	69.89%	NA
Indica III	913	10.00%	18.60%	10.30%	61.12%	NA
Indica Intermediate	786	11.10%	15.00%	10.31%	63.61%	NA
Temperate Japonica	767	95.40%	0.00%	1.43%	3.13%	NA
Tropical Japonica	504	79.00%	0.60%	4.76%	15.67%	NA
Japonica Intermediate	241	81.30%	0.00%	3.73%	14.94%	NA
VI/Aromatic	96	91.70%	0.00%	5.21%	3.12%	NA
Intermediate	90	57.80%	5.60%	3.33%	33.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0118489802	G -> A	LOC_Os01g33590.1	downstream_gene_variant ; 1524.0bp to feature; MODIFIER	silent_mutation	Average:38.745; most accessible tissue: Zhenshan97 flag leaf, score: 49.845	N	N	N	N
vg0118489802	G -> A	LOC_Os01g33590-LOC_Os01g33609	intergenic_region ; MODIFIER	silent_mutation	Average:38.745; most accessible tissue: Zhenshan97 flag leaf, score: 49.845	N	N	N	N
vg0118489802	G -> DEL	N	N	silent_mutation	Average:38.745; most accessible tissue: Zhenshan97 flag leaf, score: 49.845	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0118489802	4.63E-07	4.63E-07	mr1526	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