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Detailed information for vg0816203674:

Variant ID: vg0816203674 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 16203674
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:

TGACATGCTGATGACGATTCGCGACTCCAACCCGTGGTATGCCAACATAGTGAACCTACATGGTATCCAAGTACATACCACCAAGGGAAAATCAACGAAA[A/G]
CTAAAGTATGAAAGTTGCCGTCATATATGGGATGAGCCATACCTATATAGGGTCTGTTCCAATGTCTTACTACGAAGATTTGTGCCAACTGATGAAGGAC

Reverse complement sequence

GTCCTTCATCAGTTGGCACAAATCTTCGTAGTAAGACATTGGAACAGACCCTATATAGGTATGGCTCATCCCATATATGACGGCAACTTTCATACTTTAG[T/C]
TTTCGTTGATTTTCCCTTGGTGGTATGTACTTGGATACCATGTAGGTTCACTATGTTGGCATACCACGGGTTGGAGTCGCGAATCGTCATCAGCATGTCA

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	42.80%	38.00%	16.42%	2.84%	NA
All Indica	2759	59.60%	17.40%	20.70%	2.25%	NA
All Japonica	1512	16.70%	72.90%	7.28%	3.11%	NA
Aus	269	36.40%	33.80%	28.25%	1.49%	NA
Indica I	595	42.90%	31.80%	23.36%	2.02%	NA
Indica II	465	55.10%	18.70%	22.58%	3.66%	NA
Indica III	913	76.20%	5.90%	15.88%	1.97%	NA
Indica Intermediate	786	55.70%	19.20%	23.16%	1.91%	NA
Temperate Japonica	767	0.30%	97.70%	0.78%	1.30%	NA
Tropical Japonica	504	45.20%	35.50%	15.08%	4.17%	NA
Japonica Intermediate	241	9.50%	72.20%	11.62%	6.64%	NA
VI/Aromatic	96	3.10%	75.00%	4.17%	17.71%	NA
Intermediate	90	25.60%	53.30%	16.67%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0816203674	A -> G	LOC_Os08g26660.1	upstream_gene_variant ; 280.0bp to feature; MODIFIER	silent_mutation	Average:10.116; most accessible tissue: Zhenshan97 young leaf, score: 26.435	N	N	N	N
vg0816203674	A -> G	LOC_Os08g26650.1	downstream_gene_variant ; 454.0bp to feature; MODIFIER	silent_mutation	Average:10.116; most accessible tissue: Zhenshan97 young leaf, score: 26.435	N	N	N	N
vg0816203674	A -> G	LOC_Os08g26650-LOC_Os08g26660	intergenic_region ; MODIFIER	silent_mutation	Average:10.116; most accessible tissue: Zhenshan97 young leaf, score: 26.435	N	N	N	N
vg0816203674	A -> DEL	N	N	silent_mutation	Average:10.116; most accessible tissue: Zhenshan97 young leaf, score: 26.435	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0816203674	4.76E-06	4.76E-06	mr1387	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