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Detailed information for vg1119554312:

Variant ID: vg1119554312 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 19554312
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 124. )

Flanking Sequence (100 bp) in Reference Genome:

GCTCTTGGTCCACTTCTCGGGCTCGGCGTTGTTCCTCCGTTTCGTTGTCAGCCACGAATACGCCGAAGAAGAGAGGCGTGTAGTTATCCTCATAGCTGTC[G/A]
TCGAAGTTGTCGAAGTCGTCGTGGTCGTAGTGGTAGCCGAAGTCGTCGTAGTCGAGGATCTCGGTTGGTCGAGAACTGACACCGGGGGAGCTAAGGTAGC

Reverse complement sequence

GCTACCTTAGCTCCCCCGGTGTCAGTTCTCGACCAACCGAGATCCTCGACTACGACGACTTCGGCTACCACTACGACCACGACGACTTCGACAACTTCGA[C/T]
GACAGCTATGAGGATAACTACACGCCTCTCTTCTTCGGCGTATTCGTGGCTGACAACGAAACGGAGGAACAACGCCGAGCCCGAGAAGTGGACCAAGAGC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	95.10%	4.90%	0.00%	0.00%	NA
All Indica	2759	93.60%	6.40%	0.00%	0.00%	NA
All Japonica	1512	98.30%	1.70%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	96.00%	4.00%	0.00%	0.00%	NA
Indica II	465	77.20%	22.80%	0.00%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	94.30%	5.70%	0.00%	0.00%	NA
Temperate Japonica	767	97.70%	2.30%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	97.10%	2.90%	0.00%	0.00%	NA
VI/Aromatic	96	82.30%	17.70%	0.00%	0.00%	NA
Intermediate	90	86.70%	13.30%	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
vg1119554312	G -> A	LOC_Os11g33070.1	synonymous_variant ; p.Asp163Asp; LOW	synonymous_codon	Average:35.332; most accessible tissue: Zhenshan97 flower, score: 48.393	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1119554312	2.96E-06	NA	mr1570	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