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Detailed information for vg1127963105:

Variant ID: vg1127963105 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 27963105
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.88, G: 0.12, others allele: 0.00, population size: 49. )

Flanking Sequence (100 bp) in Reference Genome:

TATTGCATTTATTTTCGAATGTCATTGGGTGAAATTAACCTATTGTTTGCTAAAGCCCTTTTGTTCTTGATTACTTTATTCCTTGATACCTTGGGTTAAT[G/A]
TAACTTGACTAGTTGAACTTTATATATATTGGTTCAACTAGAATTTATATATGATTGCTTAGCCCTGCTTAGAAACATTAGCACACTATTGGGATAACTT

Reverse complement sequence

AAGTTATCCCAATAGTGTGCTAATGTTTCTAAGCAGGGCTAAGCAATCATATATAAATTCTAGTTGAACCAATATATATAAAGTTCAACTAGTCAAGTTA[C/T]
ATTAACCCAAGGTATCAAGGAATAAAGTAATCAAGAACAAAAGGGCTTTAGCAAACAATAGGTTAATTTCACCCAATGACATTCGAAAATAAATGCAATA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	46.00%	26.40%	10.66%	16.89%	NA
All Indica	2759	64.30%	17.60%	10.58%	7.54%	NA
All Japonica	1512	11.80%	38.00%	12.30%	37.83%	NA
Aus	269	46.10%	47.20%	4.09%	2.60%	NA
Indica I	595	64.00%	16.00%	11.60%	8.40%	NA
Indica II	465	53.10%	11.80%	18.49%	16.56%	NA
Indica III	913	74.20%	18.20%	5.26%	2.41%	NA
Indica Intermediate	786	59.50%	21.60%	11.32%	7.51%	NA
Temperate Japonica	767	5.00%	27.50%	7.04%	60.50%	NA
Tropical Japonica	504	21.60%	53.00%	17.06%	8.33%	NA
Japonica Intermediate	241	13.30%	40.20%	19.09%	27.39%	NA
VI/Aromatic	96	66.70%	22.90%	6.25%	4.17%	NA
Intermediate	90	37.80%	44.40%	10.00%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1127963105	G -> A	LOC_Os11g46150-LOC_Os11g46180	intergenic_region ; MODIFIER	silent_mutation	Average:13.288; most accessible tissue: Minghui63 young leaf, score: 20.156	N	N	N	N
vg1127963105	G -> DEL	N	N	silent_mutation	Average:13.288; most accessible tissue: Minghui63 young leaf, score: 20.156	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1127963105	NA	6.92E-06	mr1075	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
vg1127963105	3.80E-06	2.03E-10	mr1299	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
vg1127963105	6.07E-06	6.07E-06	mr1299	Jap_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
vg1127963105	NA	5.80E-06	mr1304	Jap_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
vg1127963105	NA	2.46E-08	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
vg1127963105	NA	4.83E-06	mr1427	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
vg1127963105	NA	7.35E-06	mr1634	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
vg1127963105	NA	5.13E-06	mr1724	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
vg1127963105	NA	2.31E-06	mr1727	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