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Detailed information for vg0620496522:

Variant ID: vg0620496522 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 20496522
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.67, A: 0.33, others allele: 0.00, population size: 49. )

Flanking Sequence (100 bp) in Reference Genome:

ATGTACCAAAATATTATTATCAGTAGACCCCAGAAAGGTCACACTACAATTTTGATTTATCAAGTGCATGACCCTTGATAAATTTACTCATGTGTGTGAT[G/A]
TCCGTGACTGCTTCCCGAAGCACCAACCAATTTTATTTTGAGGAAAACATCAACTAACTATGTATCACCTAAGAGGGTAATATTCAGAACTTGTGATCTT

Reverse complement sequence

AAGATCACAAGTTCTGAATATTACCCTCTTAGGTGATACATAGTTAGTTGATGTTTTCCTCAAAATAAAATTGGTTGGTGCTTCGGGAAGCAGTCACGGA[C/T]
ATCACACACATGAGTAAATTTATCAAGGGTCATGCACTTGATAAATCAAAATTGTAGTGTGACCTTTCTGGGGTCTACTGATAATAATATTTTGGTACAT

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	53.50%	41.50%	1.42%	3.51%	NA
All Indica	2759	31.10%	66.30%	2.28%	0.33%	NA
All Japonica	1512	87.00%	6.20%	0.13%	6.75%	NA
Aus	269	98.90%	1.10%	0.00%	0.00%	NA
Indica I	595	5.50%	94.10%	0.34%	0.00%	NA
Indica II	465	34.60%	63.20%	1.94%	0.22%	NA
Indica III	913	44.40%	50.30%	4.93%	0.44%	NA
Indica Intermediate	786	32.80%	65.80%	0.89%	0.51%	NA
Temperate Japonica	767	91.00%	7.00%	0.00%	1.96%	NA
Tropical Japonica	504	96.80%	0.80%	0.20%	2.18%	NA
Japonica Intermediate	241	53.50%	14.50%	0.41%	31.54%	NA
VI/Aromatic	96	42.70%	7.30%	1.04%	48.96%	NA
Intermediate	90	56.70%	33.30%	1.11%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0620496522	G -> A	LOC_Os06g35160.1	upstream_gene_variant ; 4248.0bp to feature; MODIFIER	silent_mutation	Average:22.214; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0620496522	G -> A	LOC_Os06g35165.1	upstream_gene_variant ; 697.0bp to feature; MODIFIER	silent_mutation	Average:22.214; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0620496522	G -> A	LOC_Os06g35160-LOC_Os06g35165	intergenic_region ; MODIFIER	silent_mutation	Average:22.214; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0620496522	G -> DEL	N	N	silent_mutation	Average:22.214; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0620496522	NA	2.41E-11	mr1609	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
vg0620496522	2.52E-07	2.76E-07	mr1037_2	Jap_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
vg0620496522	9.48E-07	9.43E-08	mr1062_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
vg0620496522	NA	3.78E-06	mr1167_2	Jap_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
vg0620496522	NA	1.01E-06	mr1291_2	Jap_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
vg0620496522	NA	1.61E-06	mr1726_2	Jap_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
vg0620496522	NA	5.19E-08	mr1827_2	Jap_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