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Detailed information for vg1120556042:

Variant ID: vg1120556042 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 20556042
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAAATACTTAACTAGAATGGGACATGACTCATCCAAATACAATAAATCTAGACACCTTTGTTTGTCTCTCCTCTAATTTCTCCTTATTAGGTTAACTTTC[G/A]
TTAAGATTAATTTTTTTAAGAAACCACATAAACAGAGTTGGCTAGATCGATTAGACAGAGTGTTAGCTAGCTAGCTAGCTAGATCGATTTTGATTTCTGG

Reverse complement sequence

CCAGAAATCAAAATCGATCTAGCTAGCTAGCTAGCTAACACTCTGTCTAATCGATCTAGCCAACTCTGTTTATGTGGTTTCTTAAAAAAATTAATCTTAA[C/T]
GAAAGTTAACCTAATAAGGAGAAATTAGAGGAGAGACAAACAAAGGTGTCTAGATTTATTGTATTTGGATGAGTCATGTCCCATTCTAGTTAAGTATTTT

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	99.60%	0.30%	0.11%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	98.80%	0.90%	0.33%	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	97.70%	1.70%	0.65%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	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
vg1120556042	G -> A	LOC_Os11g35070.1	upstream_gene_variant ; 3214.0bp to feature; MODIFIER	silent_mutation	Average:46.735; most accessible tissue: Minghui63 panicle, score: 78.92	N	N	N	N
vg1120556042	G -> A	LOC_Os11g35060-LOC_Os11g35070	intergenic_region ; MODIFIER	silent_mutation	Average:46.735; most accessible tissue: Minghui63 panicle, score: 78.92	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1120556042	6.43E-07	6.43E-07	mr1197	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
vg1120556042	7.13E-06	NA	mr1671	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