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Detailed information for vg0332229293:

Variant ID: vg0332229293 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 32229293
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.01, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

AGGGGTGTGTAGTTATCCTCATAGCTGTCGTCGAAGTTGTCGAGGTCGCCGTGGTTGTAGTGGTAGCCTAAATCGTCGTAGTCGAGGATCTCGGTTGGTC[G/A]
AGAACTGACGCCGGGGGAGCTGAGGTAGCCATCCAAATCTTCCGTCGAGACTGTCCCAAGAGGTTGGAGTATAACGCCAACCTCTCTGGATCTAGATTGG

Reverse complement sequence

CCAATCTAGATCCAGAGAGGTTGGCGTTATACTCCAACCTCTTGGGACAGTCTCGACGGAAGATTTGGATGGCTACCTCAGCTCCCCCGGCGTCAGTTCT[C/T]
GACCAACCGAGATCCTCGACTACGACGATTTAGGCTACCACTACAACCACGGCGACCTCGACAACTTCGACGACAGCTATGAGGATAACTACACACCCCT

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	69.00%	28.90%	2.03%	0.00%	NA
All Indica	2759	47.80%	48.80%	3.41%	0.00%	NA
All Japonica	1512	99.40%	0.50%	0.07%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	11.10%	82.20%	6.72%	0.00%	NA
Indica II	465	46.00%	49.00%	4.95%	0.00%	NA
Indica III	913	73.50%	26.10%	0.44%	0.00%	NA
Indica Intermediate	786	46.70%	49.90%	3.44%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	98.80%	1.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.40%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	85.60%	13.30%	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
vg0332229293	G -> A	LOC_Os03g56566.1	upstream_gene_variant ; 4243.0bp to feature; MODIFIER	silent_mutation	Average:41.811; most accessible tissue: Zhenshan97 root, score: 67.648	N	N	N	N
vg0332229293	G -> A	LOC_Os03g56572.1	intron_variant ; MODIFIER	silent_mutation	Average:41.811; most accessible tissue: Zhenshan97 root, score: 67.648	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0332229293	NA	6.23E-06	mr1120_2	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
vg0332229293	NA	4.71E-08	mr1212_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