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Detailed information for vg0221817321:

Variant ID: vg0221817321 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 21817321
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.02, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

TATAGTACTATTCCATACGATGTACACCAATGGTTGTGTTTGGATCCAAACTTCTAACTTTCTCTATCACATCAATCTGTCATACACACACAACTTTTCA[G/A]
TCACATCGTACTAATTTCAACCCAAACTTTCAACTTTAGAAGGAACTAAACACAACCAATATTAACTAGCTAGCACTAAGTGTCAGGATGTCGACGTAGC

Reverse complement sequence

GCTACGTCGACATCCTGACACTTAGTGCTAGCTAGTTAATATTGGTTGTGTTTAGTTCCTTCTAAAGTTGAAAGTTTGGGTTGAAATTAGTACGATGTGA[C/T]
TGAAAAGTTGTGTGTGTATGACAGATTGATGTGATAGAGAAAGTTAGAAGTTTGGATCCAAACACAACCATTGGTGTACATCGTATGGAATAGTACTATA

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	62.60%	37.30%	0.15%	0.00%	NA
All Indica	2759	68.50%	31.30%	0.14%	0.00%	NA
All Japonica	1512	60.50%	39.40%	0.07%	0.00%	NA
Aus	269	1.10%	98.90%	0.00%	0.00%	NA
Indica I	595	68.60%	31.10%	0.34%	0.00%	NA
Indica II	465	64.50%	35.50%	0.00%	0.00%	NA
Indica III	913	75.90%	24.00%	0.11%	0.00%	NA
Indica Intermediate	786	62.30%	37.50%	0.13%	0.00%	NA
Temperate Japonica	767	38.10%	61.90%	0.00%	0.00%	NA
Tropical Japonica	504	81.00%	18.80%	0.20%	0.00%	NA
Japonica Intermediate	241	89.20%	10.80%	0.00%	0.00%	NA
VI/Aromatic	96	90.60%	9.40%	0.00%	0.00%	NA
Intermediate	90	68.90%	28.90%	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
vg0221817321	G -> A	LOC_Os02g36190.1	upstream_gene_variant ; 3861.0bp to feature; MODIFIER	silent_mutation	Average:68.597; most accessible tissue: Zhenshan97 panicle, score: 83.41	N	N	N	N
vg0221817321	G -> A	LOC_Os02g36190-LOC_Os02g36200	intergenic_region ; MODIFIER	silent_mutation	Average:68.597; most accessible tissue: Zhenshan97 panicle, score: 83.41	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0221817321	NA	6.85E-07	mr1502	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
vg0221817321	NA	2.38E-08	mr1543	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
vg0221817321	NA	6.50E-07	mr1042_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
vg0221817321	2.55E-06	NA	mr1543_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
vg0221817321	4.07E-06	7.49E-10	mr1543_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