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Detailed information for vg0910744582:

Variant ID: vg0910744582 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 10744582
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, A: 0.10, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:

ATCCAAATCCAAATTCGAGTTGGGCATAAACTGTTTGATGAAAACAAAACAATGAACACACAGAAGTAGAAAACAATGAACACACAGAAGTAGAGAAACC[G/A]
TTTATTTTATTAATAATTATTCATTAACATCAATGTTTTACAAATACAATATGTTTTCACATGAGTTCGTCTTTTGCTTTCACGAAGATGCTTAATGGAG

Reverse complement sequence

CTCCATTAAGCATCTTCGTGAAAGCAAAAGACGAACTCATGTGAAAACATATTGTATTTGTAAAACATTGATGTTAATGAATAATTATTAATAAAATAAA[C/T]
GGTTTCTCTACTTCTGTGTGTTCATTGTTTTCTACTTCTGTGTGTTCATTGTTTTGTTTTCATCAAACAGTTTATGCCCAACTCGAATTTGGATTTGGAT

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	55.60%	44.10%	0.21%	0.00%	NA
All Indica	2759	84.40%	15.30%	0.29%	0.00%	NA
All Japonica	1512	0.60%	99.30%	0.13%	0.00%	NA
Aus	269	90.70%	9.30%	0.00%	0.00%	NA
Indica I	595	89.60%	10.40%	0.00%	0.00%	NA
Indica II	465	64.50%	34.60%	0.86%	0.00%	NA
Indica III	913	92.00%	8.00%	0.00%	0.00%	NA
Indica Intermediate	786	83.50%	16.00%	0.51%	0.00%	NA
Temperate Japonica	767	0.30%	99.70%	0.00%	0.00%	NA
Tropical Japonica	504	0.80%	99.20%	0.00%	0.00%	NA
Japonica Intermediate	241	1.20%	97.90%	0.83%	0.00%	NA
VI/Aromatic	96	25.00%	75.00%	0.00%	0.00%	NA
Intermediate	90	26.70%	73.30%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0910744582	G -> A	LOC_Os09g17560.1	upstream_gene_variant ; 2671.0bp to feature; MODIFIER	silent_mutation	Average:38.063; most accessible tissue: Callus, score: 63.636	N	N	N	N
vg0910744582	G -> A	LOC_Os09g17570.1	downstream_gene_variant ; 1421.0bp to feature; MODIFIER	silent_mutation	Average:38.063; most accessible tissue: Callus, score: 63.636	N	N	N	N
vg0910744582	G -> A	LOC_Os09g17560-LOC_Os09g17570	intergenic_region ; MODIFIER	silent_mutation	Average:38.063; most accessible tissue: Callus, score: 63.636	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0910744582	NA	6.16E-06	mr1425	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
vg0910744582	NA	8.42E-27	mr1903	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
vg0910744582	NA	1.66E-07	mr1004_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
vg0910744582	NA	2.18E-15	mr1162_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
vg0910744582	NA	1.16E-18	mr1168_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
vg0910744582	NA	1.85E-06	mr1227_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
vg0910744582	NA	1.45E-18	mr1712_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
vg0910744582	NA	7.52E-16	mr1717_2	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
vg0910744582	NA	2.38E-06	mr1717_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
vg0910744582	NA	4.39E-08	mr1748_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
vg0910744582	NA	9.34E-16	mr1836_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
vg0910744582	NA	1.56E-10	mr1893_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
vg0910744582	NA	2.20E-07	mr1895_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
vg0910744582	NA	2.07E-06	mr1896_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