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Detailed information for vg1208155262:

Variant ID: vg1208155262 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 8155262
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.78, G: 0.23, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:

TCACAAATGCTAGAGCAGTGCAAATATCAACGGCAGCTCTTCAGATAAATATACAGAGCCACCTGCAGTGTGTCAAGGAACGAGCTAACATGCTGCTTCG[A/G]
GAGTCCGAGTACGTGCGACTTCCAGGGCAATGAACTCGATCGTACGGTAGGTCGTCGATGCAGTCGGCGCGCGCGGTAGCTCATCTAGGTACCTACGCAT

Reverse complement sequence

ATGCGTAGGTACCTAGATGAGCTACCGCGCGCGCCGACTGCATCGACGACCTACCGTACGATCGAGTTCATTGCCCTGGAAGTCGCACGTACTCGGACTC[T/C]
CGAAGCAGCATGTTAGCTCGTTCCTTGACACACTGCAGGTGGCTCTGTATATTTATCTGAAGAGCTGCCGTTGATATTTGCACTGCTCTAGCATTTGTGA

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	24.50%	23.70%	0.68%	51.08%	NA
All Indica	2759	37.80%	6.00%	0.58%	55.60%	NA
All Japonica	1512	4.30%	49.50%	0.99%	45.17%	NA
Aus	269	0.70%	45.40%	0.00%	53.90%	NA
Indica I	595	48.20%	7.10%	0.67%	44.03%	NA
Indica II	465	51.60%	5.40%	0.22%	42.80%	NA
Indica III	913	25.60%	5.10%	0.44%	68.78%	NA
Indica Intermediate	786	35.90%	6.60%	0.89%	56.62%	NA
Temperate Japonica	767	6.30%	73.10%	0.78%	19.82%	NA
Tropical Japonica	504	1.60%	20.00%	1.19%	77.18%	NA
Japonica Intermediate	241	3.70%	36.10%	1.24%	58.92%	NA
VI/Aromatic	96	38.50%	49.00%	0.00%	12.50%	NA
Intermediate	90	14.40%	40.00%	1.11%	44.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1208155262	A -> DEL	N	N	silent_mutation	Average:32.821; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N
vg1208155262	A -> G	LOC_Os12g14310.1	downstream_gene_variant ; 1005.0bp to feature; MODIFIER	silent_mutation	Average:32.821; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N
vg1208155262	A -> G	LOC_Os12g14320.1	downstream_gene_variant ; 192.0bp to feature; MODIFIER	silent_mutation	Average:32.821; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N
vg1208155262	A -> G	LOC_Os12g14310-LOC_Os12g14320	intergenic_region ; MODIFIER	silent_mutation	Average:32.821; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1208155262	4.45E-06	4.44E-06	mr1325_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