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Detailed information for vg0627239246:

Variant ID: vg0627239246 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 27239246
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

TGACAGACGGTTTGGCTCATGGAGCTCACGGTTAGATCTATGCGGGTCATTGTCGTTTCCTTCGCCAACCTCTGGTTATGTGGGCTGTGTCACATGAGGC[G/A]
CATCATTAGTTTGTGAAGTCCGAAGCTCGTTGGGTACCGATGACGACCCTCCACCGAAGCTAGACATGTCGTCGTACGATGTAGTGTAAGGACTAAACCC

Reverse complement sequence

GGGTTTAGTCCTTACACTACATCGTACGACGACATGTCTAGCTTCGGTGGAGGGTCGTCATCGGTACCCAACGAGCTTCGGACTTCACAAACTAATGATG[C/T]
GCCTCATGTGACACAGCCCACATAACCAGAGGTTGGCGAAGGAAACGACAATGACCCGCATAGATCTAACCGTGAGCTCCATGAGCCAAACCGTCTGTCA

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	85.50%	14.40%	0.08%	0.00%	NA
All Indica	2759	75.40%	24.50%	0.14%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	95.60%	3.90%	0.50%	0.00%	NA
Indica II	465	78.10%	21.70%	0.22%	0.00%	NA
Indica III	913	61.80%	38.20%	0.00%	0.00%	NA
Indica Intermediate	786	74.20%	25.80%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	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
vg0627239246	G -> A	LOC_Os06g45030.1	downstream_gene_variant ; 3577.0bp to feature; MODIFIER	silent_mutation	Average:46.643; most accessible tissue: Minghui63 flag leaf, score: 72.472	N	N	N	N
vg0627239246	G -> A	LOC_Os06g45020-LOC_Os06g45030	intergenic_region ; MODIFIER	silent_mutation	Average:46.643; most accessible tissue: Minghui63 flag leaf, score: 72.472	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0627239246	3.73E-06	3.73E-06	mr1273	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