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Detailed information for vg1124322062:

Variant ID: vg1124322062 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24322062
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, G: 0.01, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

TTCATAGTTAAAACCGGGGGTGATGACTCCATCCCAAATTTAAAATTTTAGTACCGACTTATTACTACCAGTTATAGCTAGCAATGAACTGACACTGTTC[G/A]
ATGATAGCTATTTATTCAAACCAGCAGTGTTTGTCCACCCACTAATTAATCAGTGCAGGTTTTTGCTCCCAGCTAACACTTTGTGTTAGCATTAGTGCTA

Reverse complement sequence

TAGCACTAATGCTAACACAAAGTGTTAGCTGGGAGCAAAAACCTGCACTGATTAATTAGTGGGTGGACAAACACTGCTGGTTTGAATAAATAGCTATCAT[C/T]
GAACAGTGTCAGTTCATTGCTAGCTATAACTGGTAGTAATAAGTCGGTACTAAAATTTTAAATTTGGGATGGAGTCATCACCCCCGGTTTTAACTATGAA

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	84.20%	14.20%	0.13%	1.44%	NA
All Indica	2759	98.70%	0.80%	0.04%	0.51%	NA
All Japonica	1512	58.00%	41.90%	0.07%	0.00%	NA
Aus	269	78.10%	0.70%	1.12%	20.07%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	97.40%	2.40%	0.00%	0.22%	NA
Indica III	913	99.10%	0.10%	0.00%	0.77%	NA
Indica Intermediate	786	98.10%	1.00%	0.13%	0.76%	NA
Temperate Japonica	767	57.50%	42.40%	0.13%	0.00%	NA
Tropical Japonica	504	51.80%	48.20%	0.00%	0.00%	NA
Japonica Intermediate	241	72.60%	27.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	82.20%	16.70%	1.11%	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
vg1124322062	G -> A	LOC_Os11g40700.1	downstream_gene_variant ; 1820.0bp to feature; MODIFIER	silent_mutation	Average:46.725; most accessible tissue: Callus, score: 81.399	N	N	N	N
vg1124322062	G -> A	LOC_Os11g40690-LOC_Os11g40700	intergenic_region ; MODIFIER	silent_mutation	Average:46.725; most accessible tissue: Callus, score: 81.399	N	N	N	N
vg1124322062	G -> DEL	N	N	silent_mutation	Average:46.725; most accessible tissue: Callus, score: 81.399	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124322062	NA	5.04E-07	mr1173_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
vg1124322062	8.60E-07	NA	mr1238_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
vg1124322062	NA	5.97E-06	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
vg1124322062	NA	9.03E-07	mr1358_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
vg1124322062	1.60E-06	NA	mr1484_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
vg1124322062	NA	2.16E-08	mr1576_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
vg1124322062	NA	7.84E-07	mr1707_2	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
vg1124322062	2.71E-08	1.00E-20	mr1945_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