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Detailed information for vg0627018309:

Variant ID: vg0627018309 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 27018309
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CATCCAAGGCCGTTTGAAAAAACTCAAAAATTTCTTTCCAAGAATGGATCTAAGAGTTTGTAACAAATATTTAGCCGCCTAAACATTGTTAAATGAAAAA[G/A]
TTTTCGGCTACAAAGTTATAAAGTTATAGATCTTGTCGAGTACTACAATTTTCATAAAATGATTGTCATCTTCCGAATTTGTATTTTTTTTTTGTTTTTT

Reverse complement sequence

AAAAAACAAAAAAAAAATACAAATTCGGAAGATGACAATCATTTTATGAAAATTGTAGTACTCGACAAGATCTATAACTTTATAACTTTGTAGCCGAAAA[C/T]
TTTTTCATTTAACAATGTTTAGGCGGCTAAATATTTGTTACAAACTCTTAGATCCATTCTTGGAAAGAAATTTTTGAGTTTTTTCAAACGGCCTTGGATG

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	94.30%	5.60%	0.15%	0.00%	NA
All Indica	2759	98.40%	1.50%	0.04%	0.00%	NA
All Japonica	1512	88.00%	11.60%	0.33%	0.00%	NA
Aus	269	87.70%	12.30%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	95.90%	3.90%	0.22%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	97.10%	2.90%	0.00%	0.00%	NA
Temperate Japonica	767	99.00%	1.00%	0.00%	0.00%	NA
Tropical Japonica	504	67.70%	31.30%	0.99%	0.00%	NA
Japonica Intermediate	241	95.90%	4.10%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	85.60%	13.30%	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
vg0627018309	G -> A	LOC_Os06g44740-LOC_Os06g44750	intergenic_region ; MODIFIER	silent_mutation	Average:26.525; most accessible tissue: Callus, score: 60.616	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0627018309	3.67E-07	NA	mr1295	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