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Detailed information for vg0627565709:

Variant ID: vg0627565709 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 27565709
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTAGTTTGTTTACGAGAAAGTGACCCTCGTTTAGTGTGCATTCATATGAAATGTCGTTTTACACATATCTCTGCCATTTTCTGAACAAACATATACTCC[A/C]
TATATTTCAAAATATAAGTATTTTTAGCTATAAATATAGATAACTATATGTCCAGATTCATAACAAAAAAATTATTATATTTTAGGACAGATGTATTAGT

Reverse complement sequence

ACTAATACATCTGTCCTAAAATATAATAATTTTTTTGTTATGAATCTGGACATATAGTTATCTATATTTATAGCTAAAAATACTTATATTTTGAAATATA[T/G]
GGAGTATATGTTTGTTCAGAAAATGGCAGAGATATGTGTAAAACGACATTTCATATGAATGCACACTAAACGAGGGTCACTTTCTCGTAAACAAACTAAT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	94.90%	5.00%	0.06%	0.00%	NA
All Indica	2759	97.00%	2.90%	0.07%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	46.80%	52.80%	0.37%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	98.10%	1.90%	0.00%	0.00%	NA
Indica III	913	95.00%	4.90%	0.11%	0.00%	NA
Indica Intermediate	786	96.70%	3.20%	0.13%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	91.10%	8.90%	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
vg0627565709	A -> C	LOC_Os06g45540.1	downstream_gene_variant ; 4110.0bp to feature; MODIFIER	silent_mutation	Average:47.27; most accessible tissue: Callus, score: 86.091	N	N	N	N
vg0627565709	A -> C	LOC_Os06g45540-LOC_Os06g45550	intergenic_region ; MODIFIER	silent_mutation	Average:47.27; most accessible tissue: Callus, score: 86.091	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0627565709	NA	6.43E-07	mr1328	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
vg0627565709	NA	1.22E-11	mr1348	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