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Detailed information for vg1120290807:

Variant ID: vg1120290807 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 20290807
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.01, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

TGTAAGGCTGTGTTTAGTTACTGAAAAGAGTTGGAAGTTCGGGGAAAGTTAAAAGTTTGGAAAAAAAAAGTTGAAAATTTATGTGTATAGGAAAGTTTTG[G/A]
ATGTGATATGATGTGATGGAAAGTTGGAAGTTTGGGATATTTGGGGGTAAAGTAAACAAGACGTAAAGGAATGGAAGGAAGATGCACATGCAGGACCTGT

Reverse complement sequence

ACAGGTCCTGCATGTGCATCTTCCTTCCATTCCTTTACGTCTTGTTTACTTTACCCCCAAATATCCCAAACTTCCAACTTTCCATCACATCATATCACAT[C/T]
CAAAACTTTCCTATACACATAAATTTTCAACTTTTTTTTTCCAAACTTTTAACTTTCCCCGAACTTCCAACTCTTTTCAGTAACTAAACACAGCCTTACA

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	40.30%	15.60%	0.36%	43.78%	NA
All Indica	2759	25.90%	18.00%	0.22%	55.93%	NA
All Japonica	1512	63.50%	4.30%	0.26%	31.94%	NA
Aus	269	33.10%	61.30%	2.23%	3.35%	NA
Indica I	595	5.20%	25.40%	0.34%	69.08%	NA
Indica II	465	38.30%	19.80%	0.43%	41.51%	NA
Indica III	913	32.00%	13.50%	0.11%	54.44%	NA
Indica Intermediate	786	27.10%	16.50%	0.13%	56.23%	NA
Temperate Japonica	767	82.70%	2.10%	0.00%	15.25%	NA
Tropical Japonica	504	47.60%	9.30%	0.60%	42.46%	NA
Japonica Intermediate	241	35.70%	0.80%	0.41%	63.07%	NA
VI/Aromatic	96	91.70%	1.00%	0.00%	7.29%	NA
Intermediate	90	58.90%	10.00%	1.11%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1120290807	G -> A	LOC_Os11g34660.1	upstream_gene_variant ; 313.0bp to feature; MODIFIER	silent_mutation	Average:37.969; most accessible tissue: Callus, score: 88.72	N	N	N	N
vg1120290807	G -> A	LOC_Os11g34650-LOC_Os11g34660	intergenic_region ; MODIFIER	silent_mutation	Average:37.969; most accessible tissue: Callus, score: 88.72	N	N	N	N
vg1120290807	G -> DEL	N	N	silent_mutation	Average:37.969; most accessible tissue: Callus, score: 88.72	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1120290807	2.46E-06	2.46E-06	mr1197	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
vg1120290807	NA	1.92E-06	mr1389	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
vg1120290807	NA	1.58E-07	mr1038_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
vg1120290807	NA	1.87E-07	mr1038_2	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
vg1120290807	NA	1.96E-08	mr1389_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
vg1120290807	NA	2.68E-08	mr1389_2	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