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Detailed information for vg0334095562:

Variant ID: vg0334095562 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 34095562
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 359. )

Flanking Sequence (100 bp) in Reference Genome:

ACAGGCAAGTACAGAGGAACAATTCTAACCGCGATCAGAGTCGACGCTGATAGCCATGTTGTTCTTATTGCTTTTGCATTTGTTGAAAGCGAGAACACAT[C/G]
AAGCTGGCTTTGGTTTTTGGGGCACATTAAATTGTGTGTTGTTCAGAACAGACCAAAGGTTTGTGTTCTGCATGACCGACACGCTGGTTTGCTATCAGCG

Reverse complement sequence

CGCTGATAGCAAACCAGCGTGTCGGTCATGCAGAACACAAACCTTTGGTCTGTTCTGAACAACACACAATTTAATGTGCCCCAAAAACCAAAGCCAGCTT[G/C]
ATGTGTTCTCGCTTTCAACAAATGCAAAAGCAATAAGAACAACATGGCTATCAGCGTCGACTCTGATCGCGGTTAGAATTGTTCCTCTGTACTTGCCTGT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	98.60%	1.10%	0.25%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	96.00%	3.30%	0.73%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	99.50%	0.10%	0.39%	0.00%	NA
Tropical Japonica	504	94.40%	5.20%	0.40%	0.00%	NA
Japonica Intermediate	241	88.00%	9.50%	2.49%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	2.20%	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
vg0334095562	C -> G	LOC_Os03g59910.1	upstream_gene_variant ; 2710.0bp to feature; MODIFIER	silent_mutation	Average:31.586; most accessible tissue: Callus, score: 65.672	N	N	N	N
vg0334095562	C -> G	LOC_Os03g59920.1	downstream_gene_variant ; 3999.0bp to feature; MODIFIER	silent_mutation	Average:31.586; most accessible tissue: Callus, score: 65.672	N	N	N	N
vg0334095562	C -> G	LOC_Os03g59894.1	intron_variant ; MODIFIER	silent_mutation	Average:31.586; most accessible tissue: Callus, score: 65.672	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0334095562	5.53E-07	5.77E-08	mr1350_2	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