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Detailed information for vg0227788767:

Variant ID: vg0227788767 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 27788767
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:

CTTAGTGGTCGTGAAAAGGATTCTAAGATATTTAAAGCATTCATCTACTATTGGCTTGTGGTACCCAAAAGGTGCTAAGTTTAAGCTTGTTGGCTATTCC[G/A]
ATTCGGATTATGCCGGTTGCAAAGTGGATAGAAAGAGCACAAAATGCTTGGTAGCTCCCTTGTGTCATGGTCATCCAAGAAACAAAACTCCGTAGCCCTC

Reverse complement sequence

GAGGGCTACGGAGTTTTGTTTCTTGGATGACCATGACACAAGGGAGCTACCAAGCATTTTGTGCTCTTTCTATCCACTTTGCAACCGGCATAATCCGAAT[C/T]
GGAATAGCCAACAAGCTTAAACTTAGCACCTTTTGGGTACCACAAGCCAATAGTAGATGAATGCTTTAAATATCTTAGAATCCTTTTCACGACCACTAAG

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	92.70%	5.00%	2.35%	0.00%	NA
All Indica	2759	87.80%	8.20%	3.95%	0.00%	NA
All Japonica	1512	99.70%	0.20%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	93.80%	0.50%	5.71%	0.00%	NA
Indica II	465	77.20%	16.60%	6.24%	0.00%	NA
Indica III	913	94.00%	5.60%	0.44%	0.00%	NA
Indica Intermediate	786	82.40%	12.20%	5.34%	0.00%	NA
Temperate Japonica	767	99.60%	0.30%	0.13%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	5.60%	1.11%	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
vg0227788767	G -> A	LOC_Os02g45680.1	intron_variant ; MODIFIER	silent_mutation	Average:31.308; most accessible tissue: Minghui63 flag leaf, score: 40.473	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0227788767	NA	6.65E-06	mr1011	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
vg0227788767	NA	6.80E-06	mr1020	Ind_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
vg0227788767	NA	2.36E-07	mr1032	Ind_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
vg0227788767	NA	2.08E-07	mr1165	Ind_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
vg0227788767	NA	1.61E-07	mr1477	Ind_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
vg0227788767	NA	4.36E-08	mr1478	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
vg0227788767	NA	1.74E-06	mr1971	Ind_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
vg0227788767	NA	8.66E-06	mr1060_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
vg0227788767	NA	4.55E-06	mr1060_2	Ind_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
vg0227788767	NA	7.67E-06	mr1165_2	Ind_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
vg0227788767	NA	6.31E-08	mr1478_2	Ind_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
vg0227788767	NA	8.84E-08	mr1807_2	Ind_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
vg0227788767	NA	1.91E-06	mr1971_2	Ind_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