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Detailed information for vg0625306076:

Variant ID: vg0625306076 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 25306076
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.03, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

ACGTTTTCGCGATATCTCCCAGCTAATTACATGTTTTTTTCATGTCCTGTAGCAAATTTTGCCAAAACAAAATGCAGTATGTCTACCTACCACTACGATT[G/A]
CGTTCGTTGTCTTTAATACAAATGGAAGGTTTTCACGGTACCGAATAAAATTCGTTAAATCAAAAGCAATGAACGAGTCATATTCATCACCGTAGGGTAC

Reverse complement sequence

GTACCCTACGGTGATGAATATGACTCGTTCATTGCTTTTGATTTAACGAATTTTATTCGGTACCGTGAAAACCTTCCATTTGTATTAAAGACAACGAACG[C/T]
AATCGTAGTGGTAGGTAGACATACTGCATTTTGTTTTGGCAAAATTTGCTACAGGACATGAAAAAAACATGTAATTAGCTGGGAGATATCGCGAAAACGT

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	51.50%	42.50%	5.67%	0.36%	NA
All Indica	2759	66.80%	26.50%	6.09%	0.62%	NA
All Japonica	1512	20.00%	74.50%	5.49%	0.00%	NA
Aus	269	61.00%	35.70%	3.35%	0.00%	NA
Indica I	595	70.40%	13.90%	15.46%	0.17%	NA
Indica II	465	65.60%	27.30%	6.67%	0.43%	NA
Indica III	913	70.00%	28.60%	0.55%	0.88%	NA
Indica Intermediate	786	61.10%	33.10%	5.09%	0.76%	NA
Temperate Japonica	767	7.00%	87.20%	5.74%	0.00%	NA
Tropical Japonica	504	42.30%	53.60%	4.17%	0.00%	NA
Japonica Intermediate	241	14.90%	77.60%	7.47%	0.00%	NA
VI/Aromatic	96	80.20%	18.80%	1.04%	0.00%	NA
Intermediate	90	52.20%	40.00%	7.78%	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
vg0625306076	G -> A	LOC_Os06g42140.1	upstream_gene_variant ; 1735.0bp to feature; MODIFIER	silent_mutation	Average:52.688; most accessible tissue: Zhenshan97 flower, score: 87.73	N	N	N	N
vg0625306076	G -> A	LOC_Os06g42150.1	upstream_gene_variant ; 438.0bp to feature; MODIFIER	silent_mutation	Average:52.688; most accessible tissue: Zhenshan97 flower, score: 87.73	N	N	N	N
vg0625306076	G -> A	LOC_Os06g42150-LOC_Os06g42160	intergenic_region ; MODIFIER	silent_mutation	Average:52.688; most accessible tissue: Zhenshan97 flower, score: 87.73	N	N	N	N
vg0625306076	G -> DEL	N	N	silent_mutation	Average:52.688; most accessible tissue: Zhenshan97 flower, score: 87.73	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0625306076	NA	1.06E-06	mr1380_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
vg0625306076	NA	4.23E-06	mr1528_2	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
vg0625306076	NA	1.30E-06	mr1561_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