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Detailed information for vg0815897030:

Variant ID: vg0815897030 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 15897030
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

GTTAAGATAATCCAAGGGTAGAGTGACACACAAGCATTAACTACTCATTCTCATAATATATTATCTAAGCTAAGTGGAAAGAAAAGAGAAAAAAAATATA[T/G]
TCCTATACTTCTAATATGCATAGTATACATACATTCTAGTTAACCGAAATACTAGCTAATACCCTCTATCCGATGCCCTCCTAGTACTTCGAGAAGCCAC

Reverse complement sequence

GTGGCTTCTCGAAGTACTAGGAGGGCATCGGATAGAGGGTATTAGCTAGTATTTCGGTTAACTAGAATGTATGTATACTATGCATATTAGAAGTATAGGA[A/C]
TATATTTTTTTTCTCTTTTCTTTCCACTTAGCTTAGATAATATATTATGAGAATGAGTAGTTAATGCTTGTGTGTCACTCTACCCTTGGATTATCTTAAC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	96.90%	1.00%	1.80%	0.25%	NA
All Indica	2759	99.30%	0.10%	0.25%	0.25%	NA
All Japonica	1512	97.80%	0.70%	1.19%	0.33%	NA
Aus	269	97.40%	0.40%	2.23%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	98.90%	0.20%	0.22%	0.65%	NA
Indica III	913	99.60%	0.00%	0.22%	0.22%	NA
Indica Intermediate	786	99.00%	0.40%	0.38%	0.25%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	96.00%	1.60%	2.18%	0.20%	NA
Japonica Intermediate	241	95.00%	0.80%	2.49%	1.66%	NA
VI/Aromatic	96	21.90%	29.20%	48.96%	0.00%	NA
Intermediate	90	86.70%	5.60%	7.78%	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
vg0815897030	T -> G	LOC_Os08g26120-LOC_Os08g26140	intergenic_region ; MODIFIER	silent_mutation	Average:41.944; most accessible tissue: Zhenshan97 flag leaf, score: 72.012	N	N	N	N
vg0815897030	T -> DEL	N	N	silent_mutation	Average:41.944; most accessible tissue: Zhenshan97 flag leaf, score: 72.012	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0815897030	4.55E-08	2.59E-12	mr1188_2	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