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Detailed information for vg0819985028:

Variant ID: vg0819985028 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 19985028
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.93, G: 0.09, others allele: 0.00, population size: 91. )

Flanking Sequence (100 bp) in Reference Genome:

TCAAGAGCTCTATCAGCTTGGTTCTAAACTCTGAAGATAAATTCTTACTAATAAATGTCGGCCTCGGCCGATCGCCTGGACCTATATCTATTTCTTCCAA[A/G]
TCATCGGCCGACATAAAACCCTGACCTTGCTTGTCATCGAGATCATCTACTGTGTCATTGGTGTAGACGTTTGAACCCTCCACGACACCCTCAAAGTAAT

Reverse complement sequence

ATTACTTTGAGGGTGTCGTGGAGGGTTCAAACGTCTACACCAATGACACAGTAGATGATCTCGATGACAAGCAAGGTCAGGGTTTTATGTCGGCCGATGA[T/C]
TTGGAAGAAATAGATATAGGTCCAGGCGATCGGCCGAGGCCGACATTTATTAGTAAGAATTTATCTTCAGAGTTTAGAACCAAGCTGATAGAGCTCTTGA

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	43.00%	33.90%	4.15%	19.00%	NA
All Indica	2759	14.80%	55.10%	5.44%	24.61%	NA
All Japonica	1512	91.70%	3.00%	0.86%	4.43%	NA
Aus	269	39.00%	6.70%	6.69%	47.58%	NA
Indica I	595	17.80%	11.40%	5.04%	65.71%	NA
Indica II	465	9.70%	75.30%	7.74%	7.31%	NA
Indica III	913	11.40%	74.60%	4.71%	9.31%	NA
Indica Intermediate	786	19.60%	53.70%	5.22%	21.50%	NA
Temperate Japonica	767	98.80%	0.30%	0.00%	0.91%	NA
Tropical Japonica	504	81.70%	8.10%	1.39%	8.73%	NA
Japonica Intermediate	241	89.60%	1.20%	2.49%	6.64%	NA
VI/Aromatic	96	81.20%	3.10%	10.42%	5.21%	NA
Intermediate	90	60.00%	13.30%	5.56%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0819985028	A -> G	LOC_Os08g32260.1	synonymous_variant ; p.Asp809Asp; LOW	synonymous_codon	Average:14.29; most accessible tissue: Minghui63 root, score: 21.615	N	N	N	N
vg0819985028	A -> DEL	LOC_Os08g32260.1	N	frameshift_variant	Average:14.29; most accessible tissue: Minghui63 root, score: 21.615	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0819985028	4.60E-06	4.60E-06	mr1267_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
vg0819985028	NA	1.28E-06	mr1329_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
vg0819985028	NA	4.18E-06	mr1337_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
vg0819985028	NA	8.37E-07	mr1524_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
vg0819985028	NA	1.38E-08	mr1690_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