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Detailed information for vg0140209581:

Variant ID: vg0140209581 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 40209581
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

TCGACCACGAGTCAGACCTTCAGACCGCCATGCCGACAACAGTTAGATAGGCTACCCCAAATATTGTACTGGTGTGATTATGGTGAATAAGAGCAATACC[G/A]
GCTTCGGCCAACGGGATGTAGGGTTATTACCTGACAATTCAGGGGCCCGAACATTGTATAAAAATCCATGTCTCCATCTCTTTTATCTCAGTCTCACGTA

Reverse complement sequence

TACGTGAGACTGAGATAAAAGAGATGGAGACATGGATTTTTATACAATGTTCGGGCCCCTGAATTGTCAGGTAATAACCCTACATCCCGTTGGCCGAAGC[C/T]
GGTATTGCTCTTATTCACCATAATCACACCAGTACAATATTTGGGGTAGCCTATCTAACTGTTGTCGGCATGGCGGTCTGAAGGTCTGACTCGTGGTCGA

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	61.00%	39.00%	0.02%	0.00%	NA
All Indica	2759	92.70%	7.20%	0.04%	0.00%	NA
All Japonica	1512	2.00%	98.00%	0.00%	0.00%	NA
Aus	269	79.20%	20.80%	0.00%	0.00%	NA
Indica I	595	98.30%	1.70%	0.00%	0.00%	NA
Indica II	465	98.10%	1.90%	0.00%	0.00%	NA
Indica III	913	90.70%	9.30%	0.00%	0.00%	NA
Indica Intermediate	786	87.70%	12.20%	0.13%	0.00%	NA
Temperate Japonica	767	1.30%	98.70%	0.00%	0.00%	NA
Tropical Japonica	504	2.20%	97.80%	0.00%	0.00%	NA
Japonica Intermediate	241	3.70%	96.30%	0.00%	0.00%	NA
VI/Aromatic	96	41.70%	58.30%	0.00%	0.00%	NA
Intermediate	90	47.80%	52.20%	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
vg0140209581	G -> A	LOC_Os01g69190.1	upstream_gene_variant ; 1616.0bp to feature; MODIFIER	silent_mutation	Average:49.645; most accessible tissue: Minghui63 panicle, score: 74.563	N	N	N	N
vg0140209581	G -> A	LOC_Os01g69174.1	downstream_gene_variant ; 2699.0bp to feature; MODIFIER	silent_mutation	Average:49.645; most accessible tissue: Minghui63 panicle, score: 74.563	N	N	N	N
vg0140209581	G -> A	LOC_Os01g69174-LOC_Os01g69190	intergenic_region ; MODIFIER	silent_mutation	Average:49.645; most accessible tissue: Minghui63 panicle, score: 74.563	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0140209581	1.62E-06	1.62E-06	mr1926	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