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Detailed information for vg0809163559:

Variant ID: vg0809163559 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 9163559
Reference Allele: G	Alternative Allele: T
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.04, others allele: 0.00, population size: 28. )

Flanking Sequence (100 bp) in Reference Genome:

TGTTTTGCTAATTACATGGGATCCGGGTATTACCTATCTGCTCGCTTCTCCCATGTTTACTTGATATCTGTCCTTTGTCAACCGGGGGTAATAAATCGAC[G/T]
AGCTCATGTTACTTATGTGACCTAGCTAGAACTGTATGCTTAGCCATGCTTAATTACCACTAGCTCCGTTGATGGGATAATTACAGTATTAGACCTTTTT

Reverse complement sequence

AAAAAGGTCTAATACTGTAATTATCCCATCAACGGAGCTAGTGGTAATTAAGCATGGCTAAGCATACAGTTCTAGCTAGGTCACATAAGTAACATGAGCT[C/A]
GTCGATTTATTACCCCCGGTTGACAAAGGACAGATATCAAGTAAACATGGGAGAAGCGAGCAGATAGGTAATACCCGGATCCCATGTAATTAGCAAAACA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	73.70%	11.30%	6.90%	8.08%	NA
All Indica	2759	95.50%	0.60%	1.59%	2.28%	NA
All Japonica	1512	28.50%	33.20%	17.72%	20.57%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	89.40%	1.20%	4.87%	4.54%	NA
Indica II	465	94.80%	0.20%	0.86%	4.09%	NA
Indica III	913	99.30%	0.20%	0.33%	0.11%	NA
Indica Intermediate	786	96.10%	0.90%	1.02%	2.04%	NA
Temperate Japonica	767	11.90%	57.00%	14.73%	16.43%	NA
Tropical Japonica	504	47.80%	1.60%	24.01%	26.59%	NA
Japonica Intermediate	241	41.10%	23.70%	14.11%	21.16%	NA
VI/Aromatic	96	94.80%	0.00%	5.21%	0.00%	NA
Intermediate	90	66.70%	15.60%	8.89%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0809163559	G -> T	LOC_Os08g15120.1	upstream_gene_variant ; 2771.0bp to feature; MODIFIER	silent_mutation	Average:10.165; most accessible tissue: Callus, score: 23.213	N	N	N	N
vg0809163559	G -> T	LOC_Os08g15149.1	downstream_gene_variant ; 2409.0bp to feature; MODIFIER	silent_mutation	Average:10.165; most accessible tissue: Callus, score: 23.213	N	N	N	N
vg0809163559	G -> T	LOC_Os08g15130.1	intron_variant ; MODIFIER	silent_mutation	Average:10.165; most accessible tissue: Callus, score: 23.213	N	N	N	N
vg0809163559	G -> DEL	N	N	silent_mutation	Average:10.165; most accessible tissue: Callus, score: 23.213	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0809163559	NA	5.95E-10	Heading_date	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
vg0809163559	NA	3.76E-10	Heading_date	Jap_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
vg0809163559	NA	5.37E-06	mr1043_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
vg0809163559	NA	4.28E-06	mr1458_2	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
vg0809163559	NA	1.92E-06	mr1588_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
vg0809163559	3.36E-06	3.34E-06	mr1919_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
vg0809163559	NA	3.42E-06	mr1919_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