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Detailed information for vg1107896263:

Variant ID: vg1107896263 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 7896263
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.03, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:

GCAGAGCTAAAGATAACTTGAAAGATGGATTCATATGATTTTTTTAAAATTAACTTTCCTATATTTTTTTCTTATAAAAATGCACCGAGTATAAAAATGT[G/A]
CGCGTGGAAAACAAGGAATTAAAGTTAGGAACCATACATCCGAACATAGCCTACTACTCCCTTTATCCTGATTTGATCATCACCTAAGCAAAGAATGTAA

Reverse complement sequence

TTACATTCTTTGCTTAGGTGATGATCAAATCAGGATAAAGGGAGTAGTAGGCTATGTTCGGATGTATGGTTCCTAACTTTAATTCCTTGTTTTCCACGCG[C/T]
ACATTTTTATACTCGGTGCATTTTTATAAGAAAAAAATATAGGAAAGTTAATTTTAAAAAAATCATATGAATCCATCTTTCAAGTTATCTTTAGCTCTGC

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	81.70%	18.20%	0.04%	0.00%	NA
All Indica	2759	72.20%	27.70%	0.07%	0.00%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	71.00%	29.00%	0.00%	0.00%	NA
Indica I	595	91.40%	8.60%	0.00%	0.00%	NA
Indica II	465	71.00%	28.80%	0.22%	0.00%	NA
Indica III	913	59.90%	40.10%	0.00%	0.00%	NA
Indica Intermediate	786	72.60%	27.20%	0.13%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	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
vg1107896263	G -> A	LOC_Os11g14150.1	downstream_gene_variant ; 1248.0bp to feature; MODIFIER	silent_mutation	Average:65.783; most accessible tissue: Callus, score: 88.766	N	N	N	N
vg1107896263	G -> A	LOC_Os11g14160.1	downstream_gene_variant ; 3571.0bp to feature; MODIFIER	silent_mutation	Average:65.783; most accessible tissue: Callus, score: 88.766	N	N	N	N
vg1107896263	G -> A	LOC_Os11g14140-LOC_Os11g14150	intergenic_region ; MODIFIER	silent_mutation	Average:65.783; most accessible tissue: Callus, score: 88.766	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1107896263	1.74E-06	1.74E-06	mr1551	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