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Detailed information for vg0920481790:

Variant ID: vg0920481790 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 20481790
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

ATCATGATTCTGAGAGAGATACATTGTTGCAGTGGTTAAATTTGTTGTAATTTTTTTTCTTTATTAATATAAAATCTTAACGGTGGGGGCTTCCTCTACC[G/A]
TGGTTCTTTAAAAAAAAAACATAGAATCAAGTGAAAAAGTGGGCCTAGCCTTGCTCTATCATACAACTTCAGTATAAAGTAAAAGGTTCATACTTTAATT

Reverse complement sequence

AATTAAAGTATGAACCTTTTACTTTATACTGAAGTTGTATGATAGAGCAAGGCTAGGCCCACTTTTTCACTTGATTCTATGTTTTTTTTTTAAAGAACCA[C/T]
GGTAGAGGAAGCCCCCACCGTTAAGATTTTATATTAATAAAGAAAAAAAATTACAACAAATTTAACCACTGCAACAATGTATCTCTCTCAGAATCATGAT

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	79.20%	7.70%	10.30%	2.84%	NA
All Indica	2759	69.70%	8.50%	17.04%	4.78%	NA
All Japonica	1512	99.70%	0.10%	0.07%	0.07%	NA
Aus	269	51.70%	43.90%	4.46%	0.00%	NA
Indica I	595	78.50%	0.20%	18.99%	2.35%	NA
Indica II	465	51.00%	11.80%	29.46%	7.74%	NA
Indica III	913	70.10%	12.70%	11.39%	5.81%	NA
Indica Intermediate	786	73.70%	7.90%	14.76%	3.69%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.00%	0.41%	0.41%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	86.70%	7.80%	4.44%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0920481790	G -> DEL	N	N	silent_mutation	Average:60.215; most accessible tissue: Callus, score: 86.514	N	N	N	N
vg0920481790	G -> A	LOC_Os09g35620.1	downstream_gene_variant ; 3926.0bp to feature; MODIFIER	silent_mutation	Average:60.215; most accessible tissue: Callus, score: 86.514	N	N	N	N
vg0920481790	G -> A	LOC_Os09g35600-LOC_Os09g35620	intergenic_region ; MODIFIER	silent_mutation	Average:60.215; most accessible tissue: Callus, score: 86.514	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0920481790	NA	2.88E-06	mr1230	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
vg0920481790	1.32E-06	NA	mr1113_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
vg0920481790	2.45E-07	NA	mr1114_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
vg0920481790	5.90E-06	NA	mr1117_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
vg0920481790	4.50E-07	NA	mr1123_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
vg0920481790	7.03E-09	NA	mr1242_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
vg0920481790	5.49E-06	NA	mr1247_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
vg0920481790	1.56E-09	NA	mr1496_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