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Detailed information for vg0622686065:

Variant ID: vg0622686065 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 22686065
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAAAAGAAGAATGGCTGGATGAAACGAGTAGTATTAATAATTACTTATATTTTAGGATATAAAATTTAAATCCTTCGATTTATGGATGGAGGTAGTAGAA[G/A]
TAAATAGAAGTACATGAGTATTTGTTTAATTAGATAAAGATGTCATATTATCATATTTTTAATAGAAAATTTCTTATATTAATATATCGTAAAATCTACG

Reverse complement sequence

CGTAGATTTTACGATATATTAATATAAGAAATTTTCTATTAAAAATATGATAATATGACATCTTTATCTAATTAAACAAATACTCATGTACTTCTATTTA[C/T]
TTCTACTACCTCCATCCATAAATCGAAGGATTTAAATTTTATATCCTAAAATATAAGTAATTATTAATACTACTCGTTTCATCCAGCCATTCTTCTTTTA

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	96.70%	3.10%	0.13%	0.00%	NA
All Indica	2759	99.80%	0.20%	0.00%	0.00%	NA
All Japonica	1512	92.50%	7.30%	0.20%	0.00%	NA
Aus	269	92.20%	6.70%	1.12%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.60%	0.40%	0.00%	0.00%	NA
Temperate Japonica	767	97.50%	2.20%	0.26%	0.00%	NA
Tropical Japonica	504	85.50%	14.30%	0.20%	0.00%	NA
Japonica Intermediate	241	91.30%	8.70%	0.00%	0.00%	NA
VI/Aromatic	96	86.50%	13.50%	0.00%	0.00%	NA
Intermediate	90	97.80%	2.20%	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
vg0622686065	G -> A	LOC_Os06g38310-LOC_Os06g38320	intergenic_region ; MODIFIER	silent_mutation	Average:17.032; most accessible tissue: Zhenshan97 flower, score: 27.882	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0622686065	NA	8.79E-06	mr1829	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
vg0622686065	1.56E-06	9.50E-09	mr1829_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
vg0622686065	NA	2.58E-06	mr1842_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