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Detailed information for vg0331832899:

Variant ID: vg0331832899 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 31832899
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTCTTGCTCCAACCACCGGCGCCTCGGCTCCGACCACCGCCGTCGCTCTCTCCCTCGGCTCCGGCCACCACCGCCACCCCCTCCCCCGCTCTCTAGCTCC[G/A]
GCCACCGCCGCTGCTCTGCCCCCGCCATCGGCTCGGCCATTGCGCCTCGCGCTCTTGCAACTGATGGAGGTGGAGGGGAAGCTATCCTGTTAGGGCAACG

Reverse complement sequence

CGTTGCCCTAACAGGATAGCTTCCCCTCCACCTCCATCAGTTGCAAGAGCGCGAGGCGCAATGGCCGAGCCGATGGCGGGGGCAGAGCAGCGGCGGTGGC[C/T]
GGAGCTAGAGAGCGGGGGAGGGGGTGGCGGTGGTGGCCGGAGCCGAGGGAGAGAGCGACGGCGGTGGTCGGAGCCGAGGCGCCGGTGGTTGGAGCAAGAG

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	90.90%	8.90%	0.19%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.04%	0.00%	NA
All Japonica	1512	73.50%	26.10%	0.40%	0.00%	NA
Aus	269	98.10%	1.10%	0.74%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.10%	0.13%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	23.80%	75.20%	0.99%	0.00%	NA
Japonica Intermediate	241	94.20%	5.40%	0.41%	0.00%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	84.40%	15.60%	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
vg0331832899	G -> A	LOC_Os03g55890.1	upstream_gene_variant ; 3214.0bp to feature; MODIFIER	silent_mutation	Average:66.428; most accessible tissue: Zhenshan97 panicle, score: 90.849	N	N	N	N
vg0331832899	G -> A	LOC_Os03g55890-LOC_Os03g55920	intergenic_region ; MODIFIER	silent_mutation	Average:66.428; most accessible tissue: Zhenshan97 panicle, score: 90.849	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0331832899	1.35E-07	1.35E-07	mr1591	Jap_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