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Detailed information for vg0910147323:

Variant ID: vg0910147323 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 10147323
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.02, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

AGACGTGCAGGTAAATGGAATTTCTTGAGGACTGAGGTCAGGAGCTCACTGAAAGGAAAAGAAAGGGGAACAAGTGGACATCCTAAAAATTAATCTCTAA[A/G]
GGCCCCTTTGAATCGTAGGAATGAAAAAAAATAGAGGAATAGGAAAAACACAGGATTCGGACAGAAATACAATTGTAAAACAGAGGATTGCAAAACACAG

Reverse complement sequence

CTGTGTTTTGCAATCCTCTGTTTTACAATTGTATTTCTGTCCGAATCCTGTGTTTTTCCTATTCCTCTATTTTTTTTCATTCCTACGATTCAAAGGGGCC[T/C]
TTAGAGATTAATTTTTAGGATGTCCACTTGTTCCCCTTTCTTTTCCTTTCAGTGAGCTCCTGACCTCAGTCCTCAAGAAATTCCATTTACCTGCACGTCT

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	64.40%	35.40%	0.15%	0.00%	NA
All Indica	2759	93.20%	6.60%	0.22%	0.00%	NA
All Japonica	1512	7.30%	92.70%	0.00%	0.00%	NA
Aus	269	91.10%	8.90%	0.00%	0.00%	NA
Indica I	595	98.70%	1.20%	0.17%	0.00%	NA
Indica II	465	84.50%	15.10%	0.43%	0.00%	NA
Indica III	913	97.90%	2.10%	0.00%	0.00%	NA
Indica Intermediate	786	88.80%	10.80%	0.38%	0.00%	NA
Temperate Japonica	767	5.50%	94.50%	0.00%	0.00%	NA
Tropical Japonica	504	10.50%	89.50%	0.00%	0.00%	NA
Japonica Intermediate	241	6.60%	93.40%	0.00%	0.00%	NA
VI/Aromatic	96	68.80%	31.20%	0.00%	0.00%	NA
Intermediate	90	55.60%	43.30%	1.11%	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
vg0910147323	A -> G	LOC_Os09g16530.1	downstream_gene_variant ; 2082.0bp to feature; MODIFIER	silent_mutation	Average:84.246; most accessible tissue: Zhenshan97 root, score: 95.258	N	N	N	N
vg0910147323	A -> G	LOC_Os09g16530-LOC_Os09g16540	intergenic_region ; MODIFIER	silent_mutation	Average:84.246; most accessible tissue: Zhenshan97 root, score: 95.258	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0910147323	NA	2.81E-21	mr1195_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
vg0910147323	NA	1.51E-11	mr1195_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
vg0910147323	NA	1.18E-06	mr1403_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
vg0910147323	NA	3.30E-06	mr1528_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
vg0910147323	NA	1.53E-06	mr1691_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
vg0910147323	NA	2.56E-11	mr1705_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
vg0910147323	NA	4.93E-23	mr1708_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
vg0910147323	NA	2.62E-07	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
vg0910147323	NA	3.59E-07	mr1749_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
vg0910147323	NA	1.91E-06	mr1754_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
vg0910147323	NA	5.26E-10	mr1761_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
vg0910147323	NA	1.42E-09	mr1768_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
vg0910147323	NA	2.44E-07	mr1821_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