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Detailed information for vg0324228701:

Variant ID: vg0324228701 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 24228701
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CATGTACACATATAGTTTTACAAATTTCACAATTTTTTTTTAAATAAGACGAACGATCAAACATGTGCTAAAAAGGCAACGGTGTCAAACATTTTAAAAC[G/A]
GAGGGAGTAACAGTTACACAATGAGTGTATAGTATACCATCTTCCTTAGATACAACCTCTTAACTAAAATCTAACCTAGGGCCAGTTTGGTTTAGTGCCA

Reverse complement sequence

TGGCACTAAACCAAACTGGCCCTAGGTTAGATTTTAGTTAAGAGGTTGTATCTAAGGAAGATGGTATACTATACACTCATTGTGTAACTGTTACTCCCTC[C/T]
GTTTTAAAATGTTTGACACCGTTGCCTTTTTAGCACATGTTTGATCGTTCGTCTTATTTAAAAAAAAATTGTGAAATTTGTAAAACTATATGTGTACATG

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	76.70%	21.30%	2.01%	0.00%	NA
All Indica	2759	99.10%	0.60%	0.29%	0.00%	NA
All Japonica	1512	36.40%	58.30%	5.29%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	99.70%	0.00%	0.34%	0.00%	NA
Indica II	465	99.10%	0.90%	0.00%	0.00%	NA
Indica III	913	99.70%	0.10%	0.22%	0.00%	NA
Indica Intermediate	786	98.00%	1.50%	0.51%	0.00%	NA
Temperate Japonica	767	58.50%	34.30%	7.17%	0.00%	NA
Tropical Japonica	504	9.90%	87.70%	2.38%	0.00%	NA
Japonica Intermediate	241	21.20%	73.40%	5.39%	0.00%	NA
VI/Aromatic	96	10.40%	87.50%	2.08%	0.00%	NA
Intermediate	90	68.90%	25.60%	5.56%	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
vg0324228701	G -> A	LOC_Os03g43440.1	upstream_gene_variant ; 771.0bp to feature; MODIFIER	silent_mutation	Average:39.517; most accessible tissue: Callus, score: 59.228	N	N	N	N
vg0324228701	G -> A	LOC_Os03g43440-LOC_Os03g43460	intergenic_region ; MODIFIER	silent_mutation	Average:39.517; most accessible tissue: Callus, score: 59.228	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0324228701	1.70E-06	NA	mr1585	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
vg0324228701	7.74E-06	NA	mr1586	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
vg0324228701	NA	2.94E-12	mr1379_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
vg0324228701	NA	7.50E-06	mr1379_2	Jap_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
vg0324228701	NA	1.52E-14	mr1454_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
vg0324228701	NA	4.15E-08	mr1559_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
vg0324228701	1.85E-07	NA	mr1585_2	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