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Detailed information for vg1106023109:

Variant ID: vg1106023109 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 6023109
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

GAGTAAATACCCCTTAGTGGGTACCAACTATATAGGAAGATACGATTGGGTGGGTTATCTACTTATGCACATCTAACCTACACTAATTGAATAGACAAGT[A/G]
ATCATGAGCTATTAGATTTGCCTCGATCCTATGCGAGATAGAATAAACATGAGCTTAGAGTGGATGTTAAATTTCCTACGTTCTTCCTCTAGAATCATAG

Reverse complement sequence

CTATGATTCTAGAGGAAGAACGTAGGAAATTTAACATCCACTCTAAGCTCATGTTTATTCTATCTCGCATAGGATCGAGGCAAATCTAATAGCTCATGAT[T/C]
ACTTGTCTATTCAATTAGTGTAGGTTAGATGTGCATAAGTAGATAACCCACCCAATCGTATCTTCCTATATAGTTGGTACCCACTAAGGGGTATTTACTC

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	58.90%	40.80%	0.32%	0.00%	NA
All Indica	2759	79.60%	20.10%	0.33%	0.00%	NA
All Japonica	1512	19.40%	80.50%	0.13%	0.00%	NA
Aus	269	90.70%	7.80%	1.49%	0.00%	NA
Indica I	595	92.40%	6.70%	0.84%	0.00%	NA
Indica II	465	89.20%	10.50%	0.22%	0.00%	NA
Indica III	913	70.50%	29.50%	0.00%	0.00%	NA
Indica Intermediate	786	74.60%	25.10%	0.38%	0.00%	NA
Temperate Japonica	767	31.20%	68.60%	0.26%	0.00%	NA
Tropical Japonica	504	4.00%	96.00%	0.00%	0.00%	NA
Japonica Intermediate	241	14.10%	85.90%	0.00%	0.00%	NA
VI/Aromatic	96	11.50%	88.50%	0.00%	0.00%	NA
Intermediate	90	44.40%	55.60%	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
vg1106023109	A -> G	LOC_Os11g10910.1	intron_variant ; MODIFIER	silent_mutation	Average:26.254; most accessible tissue: Callus, score: 54.765	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1106023109	NA	3.13E-06	mr1265_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
vg1106023109	NA	7.06E-07	mr1332_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
vg1106023109	NA	1.05E-07	mr1355_2	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
vg1106023109	NA	7.18E-06	mr1655_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