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Detailed information for vg1107275983:

Variant ID: vg1107275983 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 7275983
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.07, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:

TATTTCTGTTAACATCTTTATTTTAACAAGTCAACCCAAACTAAAAACCTAAATATCTTTTAATATACAGGGTATTACACTGGCTCAACTCGGCGCGCAC[G/A]
CGTGTGGCAGTTCCACCACCACCTCAACCGCTCAATAGGTGCTCTCAATTAGCAGCCTATTTAAGTTGAGGTTCATCCTCATTGGTTTTCAAGGCGGTAT

Reverse complement sequence

ATACCGCCTTGAAAACCAATGAGGATGAACCTCAACTTAAATAGGCTGCTAATTGAGAGCACCTATTGAGCGGTTGAGGTGGTGGTGGAACTGCCACACG[C/T]
GTGCGCGCCGAGTTGAGCCAGTGTAATACCCTGTATATTAAAAGATATTTAGGTTTTTAGTTTGGGTTGACTTGTTAAAATAAAGATGTTAACAGAAATA

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	80.20%	18.80%	0.99%	0.00%	NA
All Indica	2759	67.30%	31.00%	1.63%	0.00%	NA
All Japonica	1512	98.60%	1.40%	0.00%	0.00%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	32.60%	63.90%	3.53%	0.00%	NA
Indica II	465	89.90%	9.20%	0.86%	0.00%	NA
Indica III	913	78.10%	21.00%	0.88%	0.00%	NA
Indica Intermediate	786	67.80%	30.70%	1.53%	0.00%	NA
Temperate Japonica	767	98.30%	1.70%	0.00%	0.00%	NA
Tropical Japonica	504	99.00%	1.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	85.60%	14.40%	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
vg1107275983	G -> A	LOC_Os11g12830.1	downstream_gene_variant ; 2615.0bp to feature; MODIFIER	silent_mutation	Average:46.663; most accessible tissue: Zhenshan97 flag leaf, score: 75.761	N	N	N	N
vg1107275983	G -> A	LOC_Os11g12810-LOC_Os11g12830	intergenic_region ; MODIFIER	silent_mutation	Average:46.663; most accessible tissue: Zhenshan97 flag leaf, score: 75.761	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1107275983	NA	3.52E-06	mr1551_2	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