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Detailed information for vg1104889555:

Variant ID: vg1104889555 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 4889555
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:

TAGATAATTTAGGTAGCACATGTCAACTAAAGGGGCGTTTAGCCATAAAGCTCTTTTATACGGATTGACGGGCTGGATACATGTAAATGTATGTGGAGAT[G/A]
GGCCAATGTGTTCATGTGGGCTACATTTGGCACTGAGGAGGCAAAGAGACTTACTCGGTGACTAATGGGTTGGGCTTATATGCTGGATTCCATCTAACGT

Reverse complement sequence

ACGTTAGATGGAATCCAGCATATAAGCCCAACCCATTAGTCACCGAGTAAGTCTCTTTGCCTCCTCAGTGCCAAATGTAGCCCACATGAACACATTGGCC[C/T]
ATCTCCACATACATTTACATGTATCCAGCCCGTCAATCCGTATAAAAGAGCTTTATGGCTAAACGCCCCTTTAGTTGACATGTGCTACCTAAATTATCTA

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	77.60%	22.30%	0.11%	0.00%	NA
All Indica	2759	92.50%	7.40%	0.11%	0.00%	NA
All Japonica	1512	44.70%	55.20%	0.13%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	97.10%	2.90%	0.00%	0.00%	NA
Indica II	465	96.60%	3.20%	0.22%	0.00%	NA
Indica III	913	94.60%	5.30%	0.11%	0.00%	NA
Indica Intermediate	786	84.20%	15.60%	0.13%	0.00%	NA
Temperate Japonica	767	46.30%	53.70%	0.00%	0.00%	NA
Tropical Japonica	504	30.80%	69.00%	0.20%	0.00%	NA
Japonica Intermediate	241	68.90%	30.70%	0.41%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	82.20%	17.80%	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
vg1104889555	G -> A	LOC_Os11g09150.1	upstream_gene_variant ; 2817.0bp to feature; MODIFIER	silent_mutation	Average:61.173; most accessible tissue: Zhenshan97 panicle, score: 82.888	N	N	N	N
vg1104889555	G -> A	LOC_Os11g09140-LOC_Os11g09150	intergenic_region ; MODIFIER	silent_mutation	Average:61.173; most accessible tissue: Zhenshan97 panicle, score: 82.888	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1104889555	NA	1.41E-08	Awn_length	Ind_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1104889555	NA	4.54E-07	mr1624_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
vg1104889555	NA	2.03E-09	mr1723_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
vg1104889555	NA	9.69E-07	mr1800_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