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Detailed information for vg0329570929:

Variant ID: vg0329570929 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 29570929
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

AGAATGGTTAGGATATGGATTGAACCTAAACCGTTTTAAGTGAGTTCGTTGATCCATGGTTTAATAGGGTCGATCCACCATGAGTCCATTATATCAATAG[G/A]
TTATCCATATTACGTGTTGGTAAAACTCGGACCCAAAATTTTTAAACTCGCGTTCACACTTTAAAAACTTAACGAATTCAGTTGAATTTTGGTGGGATAA

Reverse complement sequence

TTATCCCACCAAAATTCAACTGAATTCGTTAAGTTTTTAAAGTGTGAACGCGAGTTTAAAAATTTTGGGTCCGAGTTTTACCAACACGTAATATGGATAA[C/T]
CTATTGATATAATGGACTCATGGTGGATCGACCCTATTAAACCATGGATCAACGAACTCACTTAAAACGGTTTAGGTTCAATCCATATCCTAACCATTCT

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	71.80%	6.30%	12.36%	9.59%	NA
All Indica	2759	62.80%	10.50%	16.96%	9.71%	NA
All Japonica	1512	99.50%	0.20%	0.33%	0.00%	NA
Aus	269	13.80%	0.40%	26.39%	59.48%	NA
Indica I	595	96.00%	1.30%	2.35%	0.34%	NA
Indica II	465	60.00%	13.80%	18.71%	7.53%	NA
Indica III	913	42.30%	12.90%	25.08%	19.72%	NA
Indica Intermediate	786	63.40%	12.60%	17.56%	6.49%	NA
Temperate Japonica	767	99.70%	0.10%	0.13%	0.00%	NA
Tropical Japonica	504	99.40%	0.20%	0.40%	0.00%	NA
Japonica Intermediate	241	98.80%	0.40%	0.83%	0.00%	NA
VI/Aromatic	96	55.20%	0.00%	30.21%	14.58%	NA
Intermediate	90	71.10%	4.40%	12.22%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0329570929	G -> A	LOC_Os03g51650.1	upstream_gene_variant ; 4906.0bp to feature; MODIFIER	silent_mutation	Average:53.052; most accessible tissue: Minghui63 flower, score: 73.172	N	N	N	N
vg0329570929	G -> A	LOC_Os03g51650-LOC_Os03g51660	intergenic_region ; MODIFIER	silent_mutation	Average:53.052; most accessible tissue: Minghui63 flower, score: 73.172	N	N	N	N
vg0329570929	G -> DEL	N	N	silent_mutation	Average:53.052; most accessible tissue: Minghui63 flower, score: 73.172	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0329570929	NA	2.36E-06	mr1343	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
vg0329570929	NA	9.48E-09	mr1829	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
vg0329570929	4.13E-07	5.54E-14	mr1829	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
vg0329570929	NA	2.35E-07	mr1842	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
vg0329570929	NA	1.53E-07	mr1902	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
vg0329570929	NA	2.59E-10	mr1829_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