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Detailed information for vg0911114713:

Variant ID: vg0911114713 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 11114713
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.83, A: 0.17, others allele: 0.00, population size: 53. )

Flanking Sequence (100 bp) in Reference Genome:

CAACTGGGATCTAAGCCAAAGGTCTTCTCCTTCTGGATCCTTTTTCTTCAACTGAGGTTTGATGATTATTGCAAGAATGAGCATATGACATACTCAACAA[G/A]
CCACACAGTATATATGCAAGTGCATAAGAATACCAAAGGATGGCATAATATATGGTTCATTTGTGAAAGCAGCATTTAGCAAAGAGTTGAGAATTTGTAA

Reverse complement sequence

TTACAAATTCTCAACTCTTTGCTAAATGCTGCTTTCACAAATGAACCATATATTATGCCATCCTTTGGTATTCTTATGCACTTGCATATATACTGTGTGG[C/T]
TTGTTGAGTATGTCATATGCTCATTCTTGCAATAATCATCAAACCTCAGTTGAAGAAAAAGGATCCAGAAGGAGAAGACCTTTGGCTTAGATCCCAGTTG

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	34.90%	34.60%	4.44%	26.03%	NA
All Indica	2759	9.10%	56.30%	7.14%	27.40%	NA
All Japonica	1512	87.10%	1.50%	0.46%	10.98%	NA
Aus	269	8.90%	15.60%	1.86%	73.61%	NA
Indica I	595	14.50%	72.40%	1.18%	11.93%	NA
Indica II	465	11.20%	36.10%	10.54%	42.15%	NA
Indica III	913	5.60%	56.60%	9.20%	28.59%	NA
Indica Intermediate	786	8.00%	55.70%	7.25%	29.01%	NA
Temperate Japonica	767	90.90%	0.50%	0.78%	7.82%	NA
Tropical Japonica	504	88.70%	1.60%	0.00%	9.72%	NA
Japonica Intermediate	241	71.80%	4.10%	0.41%	23.65%	NA
VI/Aromatic	96	9.40%	5.20%	0.00%	85.42%	NA
Intermediate	90	53.30%	14.40%	1.11%	31.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0911114713	G -> DEL	N	N	silent_mutation	Average:38.653; most accessible tissue: Zhenshan97 flag leaf, score: 62.519	N	N	N	N
vg0911114713	G -> A	LOC_Os09g18130-LOC_Os09g18159	intergenic_region ; MODIFIER	silent_mutation	Average:38.653; most accessible tissue: Zhenshan97 flag leaf, score: 62.519	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0911114713	NA	8.36E-08	mr1895_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
vg0911114713	2.30E-06	1.44E-07	mr1895_2	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