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Detailed information for vg0818343822:

Variant ID: vg0818343822 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 18343822
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.89, T: 0.12, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

TGGTCAGAGATCATGCGGGATACTTAGGCTAGAGTTGATGCACGGTGTTGATGGAGATTCTATATGGCATACGATGGAGTTATTGTGTGCGTATGGGATG[T/C]
GGTGTCGAATTTGGAAGGAGTCTAAATTTGGTATGAGTGGTTATGTAAAGTTTGTTTCTTATACTAGAGGGTTTCCTAAGGTGTTTAGGACTCTTAGTAT

Reverse complement sequence

ATACTAAGAGTCCTAAACACCTTAGGAAACCCTCTAGTATAAGAAACAAACTTTACATAACCACTCATACCAAATTTAGACTCCTTCCAAATTCGACACC[A/G]
CATCCCATACGCACACAATAACTCCATCGTATGCCATATAGAATCTCCATCAACACCGTGCATCAACTCTAGCCTAAGTATCCCGCATGATCTCTGACCA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	52.10%	20.60%	1.46%	25.79%	NA
All Indica	2759	31.00%	25.00%	2.28%	41.75%	NA
All Japonica	1512	86.90%	9.50%	0.07%	3.57%	NA
Aus	269	55.00%	42.80%	1.49%	0.74%	NA
Indica I	595	32.30%	4.90%	1.85%	61.01%	NA
Indica II	465	78.10%	11.40%	0.65%	9.89%	NA
Indica III	913	4.70%	41.60%	2.63%	51.04%	NA
Indica Intermediate	786	32.60%	29.00%	3.18%	35.24%	NA
Temperate Japonica	767	98.30%	0.80%	0.00%	0.91%	NA
Tropical Japonica	504	69.00%	24.60%	0.20%	6.15%	NA
Japonica Intermediate	241	88.00%	5.40%	0.00%	6.64%	NA
VI/Aromatic	96	89.60%	10.40%	0.00%	0.00%	NA
Intermediate	90	67.80%	18.90%	1.11%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0818343822	T -> C	LOC_Os08g29854.1	upstream_gene_variant ; 2043.0bp to feature; MODIFIER	silent_mutation	Average:45.568; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg0818343822	T -> C	LOC_Os08g29840.1	downstream_gene_variant ; 1619.0bp to feature; MODIFIER	silent_mutation	Average:45.568; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg0818343822	T -> C	LOC_Os08g29840-LOC_Os08g29854	intergenic_region ; MODIFIER	silent_mutation	Average:45.568; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg0818343822	T -> DEL	N	N	silent_mutation	Average:45.568; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0818343822	8.94E-08	1.99E-09	mr1836	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