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Detailed information for vg1010179897:

Variant ID: vg1010179897 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 10179897
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.80, G: 0.20, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:

CGTTGGATCATCGATCCTCGCGATTCGCGAAATGACATATATAGATGGAAATACGATTGGAGCACATAGCTATAAGTCCAAACCTTGGGGCATTCACAAT[G/A]
TGCATCTAAAGTGGATAGTAAGAAATAAAATACTACTCCTACTACCAGGTTGTATACATTATGGGAGTAGTAAGTAGCTAATATCAGGTAATATGCTTAC

Reverse complement sequence

GTAAGCATATTACCTGATATTAGCTACTTACTACTCCCATAATGTATACAACCTGGTAGTAGGAGTAGTATTTTATTTCTTACTATCCACTTTAGATGCA[C/T]
ATTGTGAATGCCCCAAGGTTTGGACTTATAGCTATGTGCTCCAATCGTATTTCCATCTATATATGTCATTTCGCGAATCGCGAGGATCGATGATCCAACG

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	49.90%	49.40%	0.30%	0.40%	NA
All Indica	2759	37.40%	61.70%	0.40%	0.54%	NA
All Japonica	1512	84.60%	15.30%	0.07%	0.07%	NA
Aus	269	2.20%	97.80%	0.00%	0.00%	NA
Indica I	595	22.40%	77.00%	0.34%	0.34%	NA
Indica II	465	48.60%	50.30%	0.43%	0.65%	NA
Indica III	913	45.00%	54.10%	0.22%	0.66%	NA
Indica Intermediate	786	33.20%	65.60%	0.64%	0.51%	NA
Temperate Japonica	767	89.20%	10.80%	0.00%	0.00%	NA
Tropical Japonica	504	78.00%	22.00%	0.00%	0.00%	NA
Japonica Intermediate	241	83.80%	15.40%	0.41%	0.41%	NA
VI/Aromatic	96	2.10%	97.90%	0.00%	0.00%	NA
Intermediate	90	46.70%	47.80%	2.22%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1010179897	G -> A	LOC_Os10g20250.1	upstream_gene_variant ; 2571.0bp to feature; MODIFIER	silent_mutation	Average:71.454; most accessible tissue: Zhenshan97 panicle, score: 83.904	N	N	N	N
vg1010179897	G -> A	LOC_Os10g20260.1	downstream_gene_variant ; 525.0bp to feature; MODIFIER	silent_mutation	Average:71.454; most accessible tissue: Zhenshan97 panicle, score: 83.904	N	N	N	N
vg1010179897	G -> A	LOC_Os10g20250-LOC_Os10g20260	intergenic_region ; MODIFIER	silent_mutation	Average:71.454; most accessible tissue: Zhenshan97 panicle, score: 83.904	N	N	N	N
vg1010179897	G -> DEL	N	N	silent_mutation	Average:71.454; most accessible tissue: Zhenshan97 panicle, score: 83.904	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1010179897	NA	8.13E-12	mr1118_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
vg1010179897	NA	1.93E-09	mr1161_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
vg1010179897	NA	4.14E-13	mr1495_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
vg1010179897	5.50E-07	5.50E-07	mr1541_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