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Detailed information for vg0234310209:

Variant ID: vg0234310209 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 34310209
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.76, T: 0.25, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:

CCAGGGAAAATACACAGTGCAATTGTGCAAACTTCGTGTGTAGTGCAAACCTGAAAACTACCACATGATATATAAATGGACGTCTAAGATTTGTTCACGC[C/T]
ATCCATTTGCGTATCCTACGATAGTTTTTAGATTTACACTACATATGAAGTTTGCACTATTTATTGATGTCATATTGCCATGCACAGATATCCGATGATA

Reverse complement sequence

TATCATCGGATATCTGTGCATGGCAATATGACATCAATAAATAGTGCAAACTTCATATGTAGTGTAAATCTAAAAACTATCGTAGGATACGCAAATGGAT[G/A]
GCGTGAACAAATCTTAGACGTCCATTTATATATCATGTGGTAGTTTTCAGGTTTGCACTACACACGAAGTTTGCACAATTGCACTGTGTATTTTCCCTGG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	52.70%	46.70%	0.25%	0.34%	NA
All Indica	2759	28.30%	70.90%	0.40%	0.47%	NA
All Japonica	1512	96.80%	3.10%	0.00%	0.07%	NA
Aus	269	59.50%	40.50%	0.00%	0.00%	NA
Indica I	595	44.40%	54.60%	0.34%	0.67%	NA
Indica II	465	13.80%	84.90%	0.86%	0.43%	NA
Indica III	913	21.00%	78.50%	0.22%	0.22%	NA
Indica Intermediate	786	33.10%	65.90%	0.38%	0.64%	NA
Temperate Japonica	767	97.40%	2.50%	0.00%	0.13%	NA
Tropical Japonica	504	97.40%	2.60%	0.00%	0.00%	NA
Japonica Intermediate	241	93.80%	6.20%	0.00%	0.00%	NA
VI/Aromatic	96	34.40%	65.60%	0.00%	0.00%	NA
Intermediate	90	57.80%	38.90%	1.11%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0234310209	C -> T	LOC_Os02g56040.1	upstream_gene_variant ; 2480.0bp to feature; MODIFIER	silent_mutation	Average:66.953; most accessible tissue: Callus, score: 77.368	N	N	N	N
vg0234310209	C -> T	LOC_Os02g56060.1	upstream_gene_variant ; 2497.0bp to feature; MODIFIER	silent_mutation	Average:66.953; most accessible tissue: Callus, score: 77.368	N	N	N	N
vg0234310209	C -> T	LOC_Os02g56050.1	intron_variant ; MODIFIER	silent_mutation	Average:66.953; most accessible tissue: Callus, score: 77.368	N	N	N	N
vg0234310209	C -> DEL	N	N	silent_mutation	Average:66.953; most accessible tissue: Callus, score: 77.368	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0234310209	NA	8.56E-06	mr1041_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
vg0234310209	NA	5.29E-06	mr1294_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
vg0234310209	NA	2.93E-08	mr1418_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
vg0234310209	NA	5.39E-06	mr1420_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
vg0234310209	NA	3.72E-07	mr1488_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
vg0234310209	NA	9.55E-06	mr1497_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
vg0234310209	NA	6.82E-10	mr1506_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
vg0234310209	NA	1.87E-07	mr1604_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
vg0234310209	NA	6.59E-11	mr1659_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
vg0234310209	NA	1.96E-06	mr1992_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