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Detailed information for vg0815339015:

Variant ID: vg0815339015 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 15339015
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, C: 0.02, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

GGACCTGTAAGCATCTTCCTGCTTTGATTGCTCTAGTTACTATTGTCCTGTTAGGTAATAAAGTGCACGTTAGTATTATGATAAGTTGTAGTAACGTTAG[T/C]
GAGAGAAATAAAATTCAGTTTACCTTCGTTTCACAAGTCATGTTTACATTTTGATTTATATAGGACTCTTCGTTATGATTTGATACATGCTCCCTGGGAT

Reverse complement sequence

ATCCCAGGGAGCATGTATCAAATCATAACGAAGAGTCCTATATAAATCAAAATGTAAACATGACTTGTGAAACGAAGGTAAACTGAATTTTATTTCTCTC[A/G]
CTAACGTTACTACAACTTATCATAATACTAACGTGCACTTTATTACCTAACAGGACAATAGTAACTAGAGCAATCAAAGCAGGAAGATGCTTACAGGTCC

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	90.50%	8.60%	0.25%	0.57%	NA
All Indica	2759	99.50%	0.10%	0.40%	0.00%	NA
All Japonica	1512	75.70%	22.50%	0.00%	1.79%	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	97.80%	0.20%	1.94%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.60%	0.10%	0.25%	0.00%	NA
Temperate Japonica	767	87.70%	9.50%	0.00%	2.74%	NA
Tropical Japonica	504	52.60%	46.60%	0.00%	0.79%	NA
Japonica Intermediate	241	85.90%	13.30%	0.00%	0.83%	NA
VI/Aromatic	96	45.80%	54.20%	0.00%	0.00%	NA
Intermediate	90	84.40%	14.40%	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
vg0815339015	T -> C	LOC_Os08g25240.1	upstream_gene_variant ; 3638.0bp to feature; MODIFIER	silent_mutation	Average:24.413; most accessible tissue: Callus, score: 40.15	N	N	N	N
vg0815339015	T -> C	LOC_Os08g25250.1	intron_variant ; MODIFIER	silent_mutation	Average:24.413; most accessible tissue: Callus, score: 40.15	N	N	N	N
vg0815339015	T -> DEL	N	N	silent_mutation	Average:24.413; most accessible tissue: Callus, score: 40.15	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0815339015	NA	9.04E-06	mr1041	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
vg0815339015	NA	1.78E-06	mr1092	Jap_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
vg0815339015	NA	1.23E-06	mr1184	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
vg0815339015	NA	9.00E-06	mr1616	Jap_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
vg0815339015	NA	3.18E-07	mr1680	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
vg0815339015	NA	9.38E-07	mr1709	Jap_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
vg0815339015	NA	2.15E-09	mr1746	Jap_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
vg0815339015	NA	3.74E-07	mr1835	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
vg0815339015	NA	2.09E-08	mr1851	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
vg0815339015	NA	1.92E-06	mr1851	Jap_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
vg0815339015	4.66E-06	1.55E-14	mr1864	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
vg0815339015	NA	1.20E-09	mr1864	Jap_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
vg0815339015	NA	7.08E-06	mr1194_2	Jap_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
vg0815339015	NA	7.06E-07	mr1671_2	Jap_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
vg0815339015	NA	3.61E-08	mr1805_2	Jap_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