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Detailed information for vg0627801527:

Variant ID: vg0627801527 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 27801527
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, A: 0.01, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

AACTAAAATATCATTCAAGATATTTAAGGTAATGTAACTAATAATTATTTGATCCTAGACTGTATTTAGTGTGTACATACGTATGCTACACAACACATGC[T/A]
GATCTTTTTTCCGTAATATAGTAAATAAAAGTACATTTTCATGAACTGATTATTTCCCTAAACTTTCATATGCCCGGGTATGTAGCTTGTAGATGGGATC

Reverse complement sequence

GATCCCATCTACAAGCTACATACCCGGGCATATGAAAGTTTAGGGAAATAATCAGTTCATGAAAATGTACTTTTATTTACTATATTACGGAAAAAAGATC[A/T]
GCATGTGTTGTGTAGCATACGTATGTACACACTAAATACAGTCTAGGATCAAATAATTATTAGTTACATTACCTTAAATATCTTGAATGATATTTTAGTT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	94.10%	5.90%	0.00%	0.00%	NA
All Indica	2759	97.10%	2.90%	0.00%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	29.40%	70.60%	0.00%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	98.10%	1.90%	0.00%	0.00%	NA
Indica III	913	95.70%	4.30%	0.00%	0.00%	NA
Indica Intermediate	786	96.20%	3.80%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	0.00%	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
vg0627801527	T -> A	LOC_Os06g45910.1	downstream_gene_variant ; 2947.0bp to feature; MODIFIER	silent_mutation	Average:53.191; most accessible tissue: Callus, score: 72.628	N	N	N	N
vg0627801527	T -> A	LOC_Os06g45920.1	intron_variant ; MODIFIER	silent_mutation	Average:53.191; most accessible tissue: Callus, score: 72.628	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0627801527	NA	7.56E-06	mr1184	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
vg0627801527	NA	4.00E-09	mr1348	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