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Detailed information for vg0605538242:

Variant ID: vg0605538242 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 5538242
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.89, A: 0.11, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

GTCAAACAACTTACTCCCTTCATTCCATAATATAAGACACAACCACTTTTTCTAAATGTTCCATAATATAAGGCATGCATGCATGTAGGCAATTAACTAT[A/G]
ACCCCTTCTCCATTAAATTATTACTTTTTAAATCCTCCACTCTTATGTTCTCTAATTCTATTGGATGCATGCATTGTATTTATTAGGATGATCCAAACTA

Reverse complement sequence

TAGTTTGGATCATCCTAATAAATACAATGCATGCATCCAATAGAATTAGAGAACATAAGAGTGGAGGATTTAAAAAGTAATAATTTAATGGAGAAGGGGT[T/C]
ATAGTTAATTGCCTACATGCATGCATGCCTTATATTATGGAACATTTAGAAAAAGTGGTTGTGTCTTATATTATGGAATGAAGGGAGTAAGTTGTTTGAC

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	85.80%	14.00%	0.17%	0.00%	NA
All Indica	2759	94.60%	5.20%	0.18%	0.00%	NA
All Japonica	1512	75.60%	24.30%	0.13%	0.00%	NA
Aus	269	80.70%	19.00%	0.37%	0.00%	NA
Indica I	595	98.70%	1.00%	0.34%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	92.00%	8.00%	0.00%	0.00%	NA
Indica Intermediate	786	91.70%	7.90%	0.38%	0.00%	NA
Temperate Japonica	767	97.70%	2.10%	0.26%	0.00%	NA
Tropical Japonica	504	42.30%	57.70%	0.00%	0.00%	NA
Japonica Intermediate	241	75.10%	24.90%	0.00%	0.00%	NA
VI/Aromatic	96	18.80%	81.20%	0.00%	0.00%	NA
Intermediate	90	74.40%	25.60%	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
vg0605538242	A -> G	LOC_Os06g10620-LOC_Os06g10650	intergenic_region ; MODIFIER	silent_mutation	Average:48.182; most accessible tissue: Zhenshan97 panicle, score: 82.888	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0605538242	NA	1.61E-11	mr1454	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
vg0605538242	NA	3.29E-07	mr1308_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
vg0605538242	NA	1.18E-06	mr1554_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
vg0605538242	NA	4.48E-09	mr1578_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
vg0605538242	NA	2.43E-07	mr1819_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
vg0605538242	NA	1.66E-06	mr1819_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
vg0605538242	NA	1.66E-06	mr1860_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
vg0605538242	NA	2.59E-10	mr1952_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
vg0605538242	1.22E-06	NA	mr1968_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