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Detailed information for vg1127775608:

Variant ID: vg1127775608 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 27775608
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.75, A: 0.25, others allele: 0.00, population size: 49. )

Flanking Sequence (100 bp) in Reference Genome:

GTGCGGCCACGTAGGATTTAAACCGCTTCGAATTGAGTCGGGGGGTTATTCGCCCGGTATAAATAGTTCAGGGTTTAAAATGTCTGGTTTTACGGTTTAG[A/G]
GGGTAATTCGGTTGATCGTGATAATTCAGGGGATTAATTCGTACTTTTTCCTTATTTGAATGGTTTTTATTCATAACTTGCCAATGAGCTGTACCGCACC

Reverse complement sequence

GGTGCGGTACAGCTCATTGGCAAGTTATGAATAAAAACCATTCAAATAAGGAAAAAGTACGAATTAATCCCCTGAATTATCACGATCAACCGAATTACCC[T/C]
CTAAACCGTAAAACCAGACATTTTAAACCCTGAACTATTTATACCGGGCGAATAACCCCCCGACTCAATTCGAAGCGGTTTAAATCCTACGTGGCCGCAC

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	33.00%	30.90%	0.55%	35.61%	NA
All Indica	2759	31.00%	28.10%	0.47%	40.45%	NA
All Japonica	1512	38.90%	39.90%	0.40%	20.77%	NA
Aus	269	21.60%	11.50%	1.49%	65.43%	NA
Indica I	595	25.70%	18.70%	0.67%	54.96%	NA
Indica II	465	26.70%	10.50%	0.43%	62.37%	NA
Indica III	913	36.50%	46.50%	0.11%	16.87%	NA
Indica Intermediate	786	31.00%	24.30%	0.76%	43.89%	NA
Temperate Japonica	767	55.30%	28.00%	0.52%	16.17%	NA
Tropical Japonica	504	18.30%	51.80%	0.40%	29.56%	NA
Japonica Intermediate	241	29.90%	53.10%	0.00%	17.01%	NA
VI/Aromatic	96	26.00%	11.50%	1.04%	61.46%	NA
Intermediate	90	37.80%	40.00%	2.22%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1127775608	A -> DEL	N	N	silent_mutation	Average:39.32; most accessible tissue: Minghui63 panicle, score: 77.956	N	N	N	N
vg1127775608	A -> G	LOC_Os11g45908.1	downstream_gene_variant ; 3715.0bp to feature; MODIFIER	silent_mutation	Average:39.32; most accessible tissue: Minghui63 panicle, score: 77.956	N	N	N	N
vg1127775608	A -> G	LOC_Os11g45920.1	downstream_gene_variant ; 3716.0bp to feature; MODIFIER	silent_mutation	Average:39.32; most accessible tissue: Minghui63 panicle, score: 77.956	N	N	N	N
vg1127775608	A -> G	LOC_Os11g45908-LOC_Os11g45920	intergenic_region ; MODIFIER	silent_mutation	Average:39.32; most accessible tissue: Minghui63 panicle, score: 77.956	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1127775608	NA	8.63E-09	mr1133	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
vg1127775608	5.14E-06	5.14E-06	mr1168	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
vg1127775608	NA	1.69E-06	mr1667	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
vg1127775608	NA	1.47E-07	mr1133_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
vg1127775608	NA	5.45E-06	mr1667_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