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Detailed information for vg0727584308:

Variant ID: vg0727584308 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 27584308
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.87, G: 0.13, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

ATACGTGCGTGACCTCCTTGTATCTAAAATAAAAGAATTGCTATGGTGCTATCAATCTTATTGAGCTATTCTCATCTTAATCAAAGAGAATTCTTGTTTT[G/A]
CAAACTTTGTACAAACGCCGATGTGTCGTATTGTGATTGAGTAGCTTCCAATGGATTGACTCAATCAAATGGTTTAGAAGATTTTTCTTGCTCCCTTCGT

Reverse complement sequence

ACGAAGGGAGCAAGAAAAATCTTCTAAACCATTTGATTGAGTCAATCCATTGGAAGCTACTCAATCACAATACGACACATCGGCGTTTGTACAAAGTTTG[C/T]
AAAACAAGAATTCTCTTTGATTAAGATGAGAATAGCTCAATAAGATTGATAGCACCATAGCAATTCTTTTATTTTAGATACAAGGAGGTCACGCACGTAT

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	83.20%	16.70%	0.15%	0.00%	NA
All Indica	2759	98.00%	1.90%	0.11%	0.00%	NA
All Japonica	1512	57.80%	42.10%	0.13%	0.00%	NA
Aus	269	71.00%	29.00%	0.00%	0.00%	NA
Indica I	595	96.60%	3.20%	0.17%	0.00%	NA
Indica II	465	98.30%	1.70%	0.00%	0.00%	NA
Indica III	913	99.50%	0.50%	0.00%	0.00%	NA
Indica Intermediate	786	97.10%	2.70%	0.25%	0.00%	NA
Temperate Japonica	767	34.20%	65.60%	0.26%	0.00%	NA
Tropical Japonica	504	87.30%	12.70%	0.00%	0.00%	NA
Japonica Intermediate	241	71.40%	28.60%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	74.40%	23.30%	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
vg0727584308	G -> A	LOC_Os07g46230.1	upstream_gene_variant ; 740.0bp to feature; MODIFIER	silent_mutation	Average:61.768; most accessible tissue: Callus, score: 90.262	N	N	N	N
vg0727584308	G -> A	LOC_Os07g46220.1	downstream_gene_variant ; 23.0bp to feature; MODIFIER	silent_mutation	Average:61.768; most accessible tissue: Callus, score: 90.262	N	N	N	N
vg0727584308	G -> A	LOC_Os07g46220-LOC_Os07g46230	intergenic_region ; MODIFIER	silent_mutation	Average:61.768; most accessible tissue: Callus, score: 90.262	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0727584308	NA	6.19E-07	mr1002	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
vg0727584308	NA	1.36E-12	mr1002	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
vg0727584308	NA	9.12E-06	mr1944	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
vg0727584308	NA	1.07E-10	mr1002_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
vg0727584308	NA	4.80E-14	mr1002_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
vg0727584308	8.14E-06	NA	mr1705_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