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Detailed information for vg0627106014:

Variant ID: vg0627106014 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 27106014
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

ACTAACCCTCCACTAAATGACATTAGGGATAGGTCTACCCCCATTCTCAGCCACCCTAGTCACAACACGTCCACATAAAGAGGAGGTCTAACCCCACGTT[T/C]
GTTCGGAGCTCTCAACCACCCCATACGGCAACGAGATCCAGGGGCCACCGTCGCCGGCCGTATGGCCTCGGCTAATCTACATCGTCCCCAATGCACCTCC

Reverse complement sequence

GGAGGTGCATTGGGGACGATGTAGATTAGCCGAGGCCATACGGCCGGCGACGGTGGCCCCTGGATCTCGTTGCCGTATGGGGTGGTTGAGAGCTCCGAAC[A/G]
AACGTGGGGTTAGACCTCCTCTTTATGTGGACGTGTTGTGACTAGGGTGGCTGAGAATGGGGGTAGACCTATCCCTAATGTCATTTAGTGGAGGGTTAGT

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	59.50%	40.40%	0.08%	0.00%	NA
All Indica	2759	91.80%	8.10%	0.11%	0.00%	NA
All Japonica	1512	4.20%	95.80%	0.00%	0.00%	NA
Aus	269	34.20%	65.80%	0.00%	0.00%	NA
Indica I	595	99.30%	0.70%	0.00%	0.00%	NA
Indica II	465	91.60%	8.20%	0.22%	0.00%	NA
Indica III	913	89.70%	10.20%	0.11%	0.00%	NA
Indica Intermediate	786	88.50%	11.30%	0.13%	0.00%	NA
Temperate Japonica	767	0.90%	99.10%	0.00%	0.00%	NA
Tropical Japonica	504	9.30%	90.70%	0.00%	0.00%	NA
Japonica Intermediate	241	3.70%	96.30%	0.00%	0.00%	NA
VI/Aromatic	96	89.60%	10.40%	0.00%	0.00%	NA
Intermediate	90	42.20%	56.70%	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
vg0627106014	T -> C	LOC_Os06g44840-LOC_Os06g44860	intergenic_region ; MODIFIER	silent_mutation	Average:63.852; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0627106014	NA	3.10E-17	mr1253	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
vg0627106014	NA	2.66E-32	mr1257	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
vg0627106014	NA	2.73E-25	mr1411	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
vg0627106014	8.55E-06	8.55E-06	mr1764	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
vg0627106014	NA	9.75E-14	mr1807	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
vg0627106014	NA	6.91E-09	mr1198_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
vg0627106014	NA	6.72E-36	mr1223_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
vg0627106014	NA	8.92E-21	mr1253_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
vg0627106014	NA	8.91E-07	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
vg0627106014	NA	4.41E-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
vg0627106014	NA	9.67E-11	mr1680_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
vg0627106014	NA	6.31E-20	mr1922_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
vg0627106014	NA	7.98E-09	mr1940_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