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Detailed information for vg0914121074:

Variant ID: vg0914121074 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 14121074
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, G: 0.04, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:

GTGTTTTATTTTGTTAGGTTAAAGCTTTAAACAACAATTAAACTACACCGATTCACGAAATATTAAAGTGTGCAATCTTTCCCTGTATGCTGCATGTACC[C/G]
TTGAATGTTTTGTCATAGATAAGCGAACAGTTTCATATAATTTCTATACATGTACATGCCATTATCACTTCCAGGGGCGCTTAACATTGGTGTGCCATGT

Reverse complement sequence

ACATGGCACACCAATGTTAAGCGCCCCTGGAAGTGATAATGGCATGTACATGTATAGAAATTATATGAAACTGTTCGCTTATCTATGACAAAACATTCAA[G/C]
GGTACATGCAGCATACAGGGAAAGATTGCACACTTTAATATTTCGTGAATCGGTGTAGTTTAATTGTTGTTTAAAGCTTTAACCTAACAAAATAAAACAC

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	56.50%	43.40%	0.04%	0.00%	NA
All Indica	2759	27.50%	72.40%	0.07%	0.00%	NA
All Japonica	1512	99.40%	0.60%	0.00%	0.00%	NA
Aus	269	91.80%	8.20%	0.00%	0.00%	NA
Indica I	595	2.50%	97.50%	0.00%	0.00%	NA
Indica II	465	23.20%	76.80%	0.00%	0.00%	NA
Indica III	913	40.90%	59.10%	0.00%	0.00%	NA
Indica Intermediate	786	33.50%	66.30%	0.25%	0.00%	NA
Temperate Japonica	767	99.30%	0.70%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	74.40%	25.60%	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
vg0914121074	C -> G	LOC_Os09g23740.1	upstream_gene_variant ; 2835.0bp to feature; MODIFIER	silent_mutation	Average:78.632; most accessible tissue: Callus, score: 93.162	N	N	N	N
vg0914121074	C -> G	LOC_Os09g23750.1	upstream_gene_variant ; 4833.0bp to feature; MODIFIER	silent_mutation	Average:78.632; most accessible tissue: Callus, score: 93.162	N	N	N	N
vg0914121074	C -> G	LOC_Os09g23740-LOC_Os09g23750	intergenic_region ; MODIFIER	silent_mutation	Average:78.632; most accessible tissue: Callus, score: 93.162	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0914121074	NA	1.13E-08	mr1249	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
vg0914121074	NA	5.55E-06	mr1450	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
vg0914121074	NA	2.21E-07	mr1604	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
vg0914121074	NA	5.06E-06	mr1636	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
vg0914121074	NA	1.48E-06	mr1796	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
vg0914121074	NA	5.43E-07	mr1881	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