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Detailed information for vg1127384160:

Variant ID: vg1127384160 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 27384160
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:

CGTTTGGCAGCTGGAGATTGCTGGTGCTAGGATCCAGCCAAGAGAAATAAGAACTTACATGGGATTGAGGGAGCTGGAGTTCCCATTTTTCTAGACATTC[T/C]
TCTTCCTCCTCTTCTGATCTGTTAGATGTGTGAACAGGGATGAGCTTCTTGAATTGATATTTCCCAGCACTCATCTCATACAGAAGAATGCAGTGGGATA

Reverse complement sequence

TATCCCACTGCATTCTTCTGTATGAGATGAGTGCTGGGAAATATCAATTCAAGAAGCTCATCCCTGTTCACACATCTAACAGATCAGAAGAGGAGGAAGA[A/G]
GAATGTCTAGAAAAATGGGAACTCCAGCTCCCTCAATCCCATGTAAGTTCTTATTTCTCTTGGCTGGATCCTAGCACCAGCAATCTCCAGCTGCCAAACG

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	94.60%	5.40%	0.02%	0.00%	NA
All Indica	2759	98.70%	1.30%	0.04%	0.00%	NA
All Japonica	1512	85.80%	14.20%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.30%	0.70%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	98.90%	1.00%	0.11%	0.00%	NA
Indica Intermediate	786	97.20%	2.80%	0.00%	0.00%	NA
Temperate Japonica	767	82.90%	17.10%	0.00%	0.00%	NA
Tropical Japonica	504	91.70%	8.30%	0.00%	0.00%	NA
Japonica Intermediate	241	82.60%	17.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	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
vg1127384160	T -> C	LOC_Os11g45250.1	synonymous_variant ; p.Glu734Glu; LOW	synonymous_codon	Average:58.802; most accessible tissue: Zhenshan97 young leaf, score: 71.497	N	N	N	N
vg1127384160	T -> C	LOC_Os11g45250.2	synonymous_variant ; p.Glu535Glu; LOW	synonymous_codon	Average:58.802; most accessible tissue: Zhenshan97 young leaf, score: 71.497	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1127384160	1.36E-07	NA	mr1900	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