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Detailed information for vg1117425028:

Variant ID: vg1117425028 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 17425028
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.94, C: 0.06, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

TAGAAAATTATAAAACCATTGCTAATGAAAACAATTTATGGAGAAATCATATATTGTAGATGTTAAAACATAGTCTACGACACATGCCCGCGCGAATATG[T/C]
GGGCTATCTTCCTAGTTATTTTAAAAAAGGTAGCAATCCCAGAGCGGCCGCATTTTTGTCCGCTGTCTGAAGATCCTCCAGCTCCTCTCGCTGTCTCACA

Reverse complement sequence

TGTGAGACAGCGAGAGGAGCTGGAGGATCTTCAGACAGCGGACAAAAATGCGGCCGCTCTGGGATTGCTACCTTTTTTAAAATAACTAGGAAGATAGCCC[A/G]
CATATTCGCGCGGGCATGTGTCGTAGACTATGTTTTAACATCTACAATATATGATTTCTCCATAAATTGTTTTCATTAGCAATGGTTTTATAATTTTCTA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	84.00%	14.60%	1.40%	0.00%	NA
All Indica	2759	82.90%	15.00%	2.10%	0.00%	NA
All Japonica	1512	85.50%	14.20%	0.26%	0.00%	NA
Aus	269	94.80%	5.20%	0.00%	0.00%	NA
Indica I	595	79.50%	13.60%	6.89%	0.00%	NA
Indica II	465	93.50%	6.20%	0.22%	0.00%	NA
Indica III	913	77.80%	22.00%	0.22%	0.00%	NA
Indica Intermediate	786	85.20%	13.00%	1.78%	0.00%	NA
Temperate Japonica	767	99.50%	0.50%	0.00%	0.00%	NA
Tropical Japonica	504	62.90%	36.70%	0.40%	0.00%	NA
Japonica Intermediate	241	88.40%	10.80%	0.83%	0.00%	NA
VI/Aromatic	96	77.10%	20.80%	2.08%	0.00%	NA
Intermediate	90	68.90%	28.90%	2.22%	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
vg1117425028	T -> C	LOC_Os11g29980.1	downstream_gene_variant ; 517.0bp to feature; MODIFIER	silent_mutation	Average:37.335; most accessible tissue: Minghui63 young leaf, score: 63.571	N	N	N	N
vg1117425028	T -> C	LOC_Os11g29970-LOC_Os11g29980	intergenic_region ; MODIFIER	silent_mutation	Average:37.335; most accessible tissue: Minghui63 young leaf, score: 63.571	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1117425028	NA	4.26E-06	mr1662	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