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Detailed information for vg0727501372:

Variant ID: vg0727501372 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 27501372
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: 108. )

Flanking Sequence (100 bp) in Reference Genome:

ATTACAGAATCTACTTATAAACTGCGAGATGAATTTATTAAGCCTAATTAATCCATCATTAGCAAATATTTACTGTAGCTCCACATTGTCAAATCATGTA[G/A]
CAATTAAGCTTAAAAAGATTTGTCTCGCAAATTAGTCGCAATATGTGTAATTAGTTAATTTTTTTAGCTTATATTTTATACTTCATACAGGTGTTCAAAC

Reverse complement sequence

GTTTGAACACCTGTATGAAGTATAAAATATAAGCTAAAAAAATTAACTAATTACACATATTGCGACTAATTTGCGAGACAAATCTTTTTAAGCTTAATTG[C/T]
TACATGATTTGACAATGTGGAGCTACAGTAAATATTTGCTAATGATGGATTAATTAGGCTTAATAAATTCATCTCGCAGTTTATAAGTAGATTCTGTAAT

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	78.40%	12.30%	2.71%	6.64%	NA
All Indica	2759	93.00%	4.10%	0.87%	2.03%	NA
All Japonica	1512	47.90%	30.20%	6.61%	15.21%	NA
Aus	269	90.70%	0.40%	0.00%	8.92%	NA
Indica I	595	96.60%	1.70%	0.34%	1.34%	NA
Indica II	465	98.10%	1.30%	0.22%	0.43%	NA
Indica III	913	97.60%	0.70%	0.44%	1.31%	NA
Indica Intermediate	786	81.80%	11.70%	2.16%	4.33%	NA
Temperate Japonica	767	67.50%	20.90%	3.91%	7.69%	NA
Tropical Japonica	504	24.60%	41.10%	9.92%	24.40%	NA
Japonica Intermediate	241	34.40%	37.30%	8.30%	19.92%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	82.20%	8.90%	4.44%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0727501372	G -> DEL	N	N	silent_mutation	Average:48.469; most accessible tissue: Zhenshan97 panicle, score: 82.336	N	N	N	N
vg0727501372	G -> A	LOC_Os07g46080.1	upstream_gene_variant ; 465.0bp to feature; MODIFIER	silent_mutation	Average:48.469; most accessible tissue: Zhenshan97 panicle, score: 82.336	N	N	N	N
vg0727501372	G -> A	LOC_Os07g46070.1	downstream_gene_variant ; 3676.0bp to feature; MODIFIER	silent_mutation	Average:48.469; most accessible tissue: Zhenshan97 panicle, score: 82.336	N	N	N	N
vg0727501372	G -> A	LOC_Os07g46070-LOC_Os07g46080	intergenic_region ; MODIFIER	silent_mutation	Average:48.469; most accessible tissue: Zhenshan97 panicle, score: 82.336	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0727501372	NA	1.02E-08	mr1002	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
vg0727501372	NA	2.20E-06	mr1369_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
vg0727501372	5.25E-06	5.25E-06	mr1369_2	Ind_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
vg0727501372	3.95E-06	8.10E-07	mr1528_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
vg0727501372	NA	4.62E-06	mr1648_2	Ind_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
vg0727501372	5.78E-06	5.78E-06	mr1652_2	Ind_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
vg0727501372	7.51E-06	7.50E-06	mr1697_2	Ind_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