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Detailed information for vg0814668918:

Variant ID: vg0814668918 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 14668918
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

CTGTCTTTCTCATGCCTCTGCTTGGCTGGAGCTAGAAGACAACATGATGGCCCTCAGATCAATTACAAATTAGGCCGAGTTTAGTCCCAAACTTTTTCTT[T/C]
AAACTTTCAACTTTTCTATCACATCAAAACTTTCCTACACACACAAACTTTCAACTTTTCCGTCACATCATTCCAATCTTAACCAAACTTCCAATTTTAG

Reverse complement sequence

CTAAAATTGGAAGTTTGGTTAAGATTGGAATGATGTGACGGAAAAGTTGAAAGTTTGTGTGTGTAGGAAAGTTTTGATGTGATAGAAAAGTTGAAAGTTT[A/G]
AAGAAAAAGTTTGGGACTAAACTCGGCCTAATTTGTAATTGATCTGAGGGCCATCATGTTGTCTTCTAGCTCCAGCCAAGCAGAGGCATGAGAAAGACAG

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	90.90%	9.00%	0.08%	0.00%	NA
All Indica	2759	96.50%	3.50%	0.00%	0.00%	NA
All Japonica	1512	78.90%	21.00%	0.13%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	97.20%	2.80%	0.00%	0.00%	NA
Indica III	913	95.50%	4.50%	0.00%	0.00%	NA
Indica Intermediate	786	94.70%	5.30%	0.00%	0.00%	NA
Temperate Japonica	767	66.90%	33.00%	0.13%	0.00%	NA
Tropical Japonica	504	94.60%	5.20%	0.20%	0.00%	NA
Japonica Intermediate	241	84.20%	15.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	83.30%	14.40%	2.22%	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
vg0814668918	T -> C	LOC_Os08g24300.1	upstream_gene_variant ; 4912.0bp to feature; MODIFIER	silent_mutation	Average:63.722; most accessible tissue: Zhenshan97 panicle, score: 83.904	N	N	N	N
vg0814668918	T -> C	LOC_Os08g24310.1	upstream_gene_variant ; 4101.0bp to feature; MODIFIER	silent_mutation	Average:63.722; most accessible tissue: Zhenshan97 panicle, score: 83.904	N	N	N	N
vg0814668918	T -> C	LOC_Os08g24300-LOC_Os08g24310	intergenic_region ; MODIFIER	silent_mutation	Average:63.722; most accessible tissue: Zhenshan97 panicle, score: 83.904	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0814668918	8.05E-06	1.48E-09	mr1134	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
vg0814668918	6.78E-06	2.79E-08	mr1135	Ind_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
vg0814668918	1.96E-06	9.38E-08	mr1672	Ind_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
vg0814668918	NA	7.55E-09	mr1769	Ind_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
vg0814668918	NA	3.36E-06	mr1134_2	Ind_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
vg0814668918	NA	5.68E-10	mr1769_2	Ind_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
vg0814668918	NA	1.48E-06	mr1951_2	Ind_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