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Detailed information for vg0627801883:

Variant ID: vg0627801883 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 27801883
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, T: 0.07, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

GGACAAAAATGATGGAGATTGGTGGCTTTACTTTGGATATGACATCAACAATCTCAATCGAGTTGGATTTTGGCCAAAGAATATTTTTAATCGTATGGTA[G/T]
ATCATGCTACTCGTATAAGGTGGGCTGGCTATGCTCAATCCTACAAAGGGAGCTCCAGTCCCCCAATGGGCAATGGGCAATTTCCAGGAAAAATGTCAGC

Reverse complement sequence

GCTGACATTTTTCCTGGAAATTGCCCATTGCCCATTGGGGGACTGGAGCTCCCTTTGTAGGATTGAGCATAGCCAGCCCACCTTATACGAGTAGCATGAT[C/A]
TACCATACGATTAAAAATATTCTTTGGCCAAAATCCAACTCGATTGAGATTGTTGATGTCATATCCAAAGTAAAGCCACCAATCTCCATCATTTTTGTCC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.90%	6.10%	0.00%	0.00%	NA
All Indica	2759	97.00%	3.00%	0.00%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	28.30%	71.70%	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	95.30%	4.70%	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
vg0627801883	G -> T	LOC_Os06g45920.1	missense_variant ; p.Asp151Tyr; MODERATE	nonsynonymous_codon ; D151Y	Average:63.875; most accessible tissue: Zhenshan97 flower, score: 78.853	unknown	unknown	TOLERATED	0.05

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0627801883	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
vg0627801883	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