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Detailed information for vg1122441548:

Variant ID: vg1122441548 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 22441548
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 300. )

Flanking Sequence (100 bp) in Reference Genome:

TTATAGATATTGAATATTTCATTTTATACTTCCTAAAGAAAACATAATCATTGCTTCAGGATGCAATGATTTCCCAAGCTTAAACCCCTATGCTTCCTCG[G/A]
TCATCCATGCGTCTATATTGTGTTCTCCTATACAACTCCACTTGTCATTAGTCATGCACTGTTCTTTTTTTAGAGGGAGTATATTAGATCAATGGATAGT

Reverse complement sequence

ACTATCCATTGATCTAATATACTCCCTCTAAAAAAAGAACAGTGCATGACTAATGACAAGTGGAGTTGTATAGGAGAACACAATATAGACGCATGGATGA[C/T]
CGAGGAAGCATAGGGGTTTAAGCTTGGGAAATCATTGCATCCTGAAGCAATGATTATGTTTTCTTTAGGAAGTATAAAATGAAATATTCAATATCTATAA

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	99.20%	0.80%	0.02%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	97.40%	2.60%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	98.60%	1.30%	0.13%	0.00%	NA
Tropical Japonica	504	95.00%	5.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	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
vg1122441548	G -> A	LOC_Os11g37870.1	upstream_gene_variant ; 699.0bp to feature; MODIFIER	silent_mutation	Average:37.248; most accessible tissue: Callus, score: 67.196	N	N	N	N
vg1122441548	G -> A	LOC_Os11g37860-LOC_Os11g37870	intergenic_region ; MODIFIER	silent_mutation	Average:37.248; most accessible tissue: Callus, score: 67.196	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1122441548	1.46E-06	9.66E-07	mr1113	Jap_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