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Detailed information for vg1227054616:

Variant ID: vg1227054616 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 27054616
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, T: 0.00, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:

CACGTTGTTATATATTCTGAGTAGCTCTTACCACAAATGTTCTATATGGAGTTGCATTTGATAAAACAACTGATGTCAGCACCTCTGTTCCATCAGCCAA[A/T]
ACTACCTACAAGTTCCCATAATTTCAAGAGGTTCAAAGAAATGAAATAGGAGTACCATTTATCGGTTAGTCAAAGAACTTACCCCCTGTACCTTCCCAGA

Reverse complement sequence

TCTGGGAAGGTACAGGGGGTAAGTTCTTTGACTAACCGATAAATGGTACTCCTATTTCATTTCTTTGAACCTCTTGAAATTATGGGAACTTGTAGGTAGT[T/A]
TTGGCTGATGGAACAGAGGTGCTGACATCAGTTGTTTTATCAAATGCAACTCCATATAGAACATTTGTGGTAAGAGCTACTCAGAATATATAACAACGTG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	78.20%	21.60%	0.13%	0.00%	NA
All Indica	2759	63.70%	36.10%	0.18%	0.00%	NA
All Japonica	1512	99.70%	0.20%	0.07%	0.00%	NA
Aus	269	96.30%	3.70%	0.00%	0.00%	NA
Indica I	595	88.20%	11.60%	0.17%	0.00%	NA
Indica II	465	49.90%	50.10%	0.00%	0.00%	NA
Indica III	913	58.70%	41.10%	0.22%	0.00%	NA
Indica Intermediate	786	59.20%	40.60%	0.25%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.40%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	85.60%	14.40%	0.00%	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
vg1227054616	A -> T	LOC_Os12g43590.1	synonymous_variant ; p.Val331Val; LOW	synonymous_codon	Average:50.217; most accessible tissue: Zhenshan97 flower, score: 62.865	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1227054616	NA	2.22E-06	mr1345	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
vg1227054616	NA	7.43E-06	mr1500	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
vg1227054616	NA	2.13E-06	mr1531	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
vg1227054616	NA	1.31E-06	mr1729	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
vg1227054616	8.17E-06	NA	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
vg1227054616	2.11E-06	2.32E-07	mr1807	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
vg1227054616	NA	3.49E-06	mr1974	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
vg1227054616	NA	9.16E-06	mr1974	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
vg1227054616	NA	7.90E-06	mr1984	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
vg1227054616	NA	2.21E-06	mr1984	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
vg1227054616	NA	5.98E-09	mr1322_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
vg1227054616	NA	2.13E-08	mr1527_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
vg1227054616	NA	1.72E-08	mr1690_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
vg1227054616	NA	3.96E-06	mr1992_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