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Detailed information for vg1125867362:

Variant ID: vg1125867362 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25867362
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.92, G: 0.07, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:

TCGAATAAATAAGATCGTCAACTACAATTATAGATTGCGTCGAGCCATAGAACTTTGATATAGAGCATATCTCGCTCATTTGAAAAACTCGAAAGATCTC[A/G]
TTAAGAGCTACAATTTTCATATTGAGCGTGTCACCATCTAACTTTATATGAAAGGGTTGCGACTATTTTATTCCATTGGTGCTCACATATTTAGCATGGT

Reverse complement sequence

ACCATGCTAAATATGTGAGCACCAATGGAATAAAATAGTCGCAACCCTTTCATATAAAGTTAGATGGTGACACGCTCAATATGAAAATTGTAGCTCTTAA[T/C]
GAGATCTTTCGAGTTTTTCAAATGAGCGAGATATGCTCTATATCAAAGTTCTATGGCTCGACGCAATCTATAATTGTAGTTGACGATCTTATTTATTCGA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	57.20%	6.40%	1.97%	34.45%	NA
All Indica	2759	61.90%	9.10%	2.28%	26.79%	NA
All Japonica	1512	49.50%	2.50%	0.73%	47.29%	NA
Aus	269	47.20%	5.60%	6.32%	40.89%	NA
Indica I	595	93.90%	2.50%	0.67%	2.86%	NA
Indica II	465	39.40%	4.50%	5.59%	50.54%	NA
Indica III	913	57.80%	9.30%	1.31%	31.54%	NA
Indica Intermediate	786	55.60%	16.40%	2.67%	25.32%	NA
Temperate Japonica	767	65.40%	4.30%	0.26%	29.99%	NA
Tropical Japonica	504	24.60%	0.40%	0.99%	74.01%	NA
Japonica Intermediate	241	50.60%	1.20%	1.66%	46.47%	NA
VI/Aromatic	96	58.30%	0.00%	1.04%	40.62%	NA
Intermediate	90	70.00%	1.10%	1.11%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1125867362	A -> DEL	N	N	silent_mutation	Average:29.379; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg1125867362	A -> G	LOC_Os11g42910.1	downstream_gene_variant ; 1126.0bp to feature; MODIFIER	silent_mutation	Average:29.379; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg1125867362	A -> G	LOC_Os11g42910-LOC_Os11g42920	intergenic_region ; MODIFIER	silent_mutation	Average:29.379; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125867362	5.29E-06	NA	mr1133	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
vg1125867362	NA	5.64E-11	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
vg1125867362	NA	2.60E-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
vg1125867362	NA	5.83E-12	mr1133_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
vg1125867362	NA	5.31E-09	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