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Detailed information for vg0827768147:

Variant ID: vg0827768147 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 27768147
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.82, C: 0.18, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

TACCACGACGACACTTAGAGTTGAAACCAATCCTACTGTCCCTTTATGCCGCCCTGGCAAGGCCTCCGAGGAACCTAAGGGAACTTCGGCTGGGCACGCC[T/C]
AGAGCGGATAAGGCCTTGTCAGGTAATGCAGAGATGAACGACCATGTAAGATCTGGTCATGTAAGAGTTCTCACCGTGCGTATTAACCAAGCCGTGTAAT

Reverse complement sequence

ATTACACGGCTTGGTTAATACGCACGGTGAGAACTCTTACATGACCAGATCTTACATGGTCGTTCATCTCTGCATTACCTGACAAGGCCTTATCCGCTCT[A/G]
GGCGTGCCCAGCCGAAGTTCCCTTAGGTTCCTCGGAGGCCTTGCCAGGGCGGCATAAAGGGACAGTAGGATTGGTTTCAACTCTAAGTGTCGTCGTGGTA

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	60.40%	17.20%	22.34%	0.00%	NA
All Indica	2759	39.70%	27.40%	32.91%	0.00%	NA
All Japonica	1512	98.80%	0.50%	0.73%	0.00%	NA
Aus	269	39.40%	14.50%	46.10%	0.00%	NA
Indica I	595	24.40%	53.80%	21.85%	0.00%	NA
Indica II	465	52.50%	15.30%	32.26%	0.00%	NA
Indica III	913	45.80%	18.00%	36.25%	0.00%	NA
Indica Intermediate	786	36.60%	25.60%	37.79%	0.00%	NA
Temperate Japonica	767	99.00%	0.70%	0.39%	0.00%	NA
Tropical Japonica	504	98.60%	0.20%	1.19%	0.00%	NA
Japonica Intermediate	241	98.80%	0.40%	0.83%	0.00%	NA
VI/Aromatic	96	95.80%	2.10%	2.08%	0.00%	NA
Intermediate	90	76.70%	11.10%	12.22%	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
vg0827768147	T -> C	LOC_Os08g44080-LOC_Os08g44110	intergenic_region ; MODIFIER	silent_mutation	Average:39.647; most accessible tissue: Minghui63 young leaf, score: 56.213	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0827768147	NA	2.10E-11	mr1307	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
vg0827768147	NA	9.41E-08	mr1569	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
vg0827768147	NA	1.60E-08	mr1607	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
vg0827768147	NA	2.23E-06	mr1646	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
vg0827768147	NA	7.87E-06	mr1898	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
vg0827768147	NA	1.08E-09	mr1986	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