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Detailed information for vg0907977858:

Variant ID: vg0907977858 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 7977858
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: 0.03, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:

AATATATATTTTTTTCATAAAATAGACGGTAGATTTTAATATACTACTAATGTGATAGGAATGTCCCTCAAATTTAAATAAAAATCCCTTTGTCCTGGTC[A/G]
ATTTGTGGTAGAGAATAGACGATTTGTATATGAAGTTAGTAATAAGTTCATCTCAAATTTTAATGGACTACATACAATATTATGTTGTTTTTCAAATGAG

Reverse complement sequence

CTCATTTGAAAAACAACATAATATTGTATGTAGTCCATTAAAATTTGAGATGAACTTATTACTAACTTCATATACAAATCGTCTATTCTCTACCACAAAT[T/C]
GACCAGGACAAAGGGATTTTTATTTAAATTTGAGGGACATTCCTATCACATTAGTAGTATATTAAAATCTACCGTCTATTTTATGAAAAAAATATATATT

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	80.50%	19.50%	0.06%	0.00%	NA
All Indica	2759	93.60%	6.30%	0.07%	0.00%	NA
All Japonica	1512	52.10%	47.90%	0.07%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	93.60%	6.20%	0.17%	0.00%	NA
Indica II	465	89.70%	10.10%	0.22%	0.00%	NA
Indica III	913	99.00%	1.00%	0.00%	0.00%	NA
Indica Intermediate	786	89.60%	10.40%	0.00%	0.00%	NA
Temperate Japonica	767	37.70%	62.20%	0.13%	0.00%	NA
Tropical Japonica	504	78.80%	21.20%	0.00%	0.00%	NA
Japonica Intermediate	241	41.90%	58.10%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	78.90%	21.10%	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
vg0907977858	A -> G	LOC_Os09g13660.1	downstream_gene_variant ; 3522.0bp to feature; MODIFIER	silent_mutation	Average:27.563; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0907977858	A -> G	LOC_Os09g13650-LOC_Os09g13660	intergenic_region ; MODIFIER	silent_mutation	Average:27.563; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0907977858	NA	9.59E-08	mr1002	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
vg0907977858	NA	2.45E-09	mr1002	Jap_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
vg0907977858	NA	7.30E-06	mr1559	Jap_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
vg0907977858	NA	2.88E-11	mr1002_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
vg0907977858	NA	6.85E-10	mr1002_2	Jap_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
vg0907977858	NA	3.52E-06	mr1011_2	Jap_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
vg0907977858	NA	1.69E-08	mr1330_2	Jap_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
vg0907977858	NA	1.79E-08	mr1378_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
vg0907977858	NA	2.31E-08	mr1379_2	Jap_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
vg0907977858	NA	8.29E-06	mr1409_2	Jap_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
vg0907977858	2.79E-07	2.79E-07	mr1548_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
vg0907977858	NA	2.24E-07	mr1559_2	Jap_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
vg0907977858	NA	2.16E-08	mr1709_2	Jap_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
vg0907977858	NA	7.28E-09	mr1805_2	Jap_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