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Detailed information for vg0802255218:

Variant ID: vg0802255218 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 2255218
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TACAGGGAAATTGATTTCATCCGATACCCTCTCGTTTCGTATATGCCACCTGAATATTCACTAAAAGAATACAAAAGAAGTTAGCAACATATATTAATAT[G/A]
AAATATATCACTCCACAAATATGCAGGTTTAAATTCAGCTTCTACAAGTTGTAACAAAAATAACAAATATAGTTGTGAATGTGCAATAATTATTTTCACT

Reverse complement sequence

AGTGAAAATAATTATTGCACATTCACAACTATATTTGTTATTTTTGTTACAACTTGTAGAAGCTGAATTTAAACCTGCATATTTGTGGAGTGATATATTT[C/T]
ATATTAATATATGTTGCTAACTTCTTTTGTATTCTTTTAGTGAATATTCAGGTGGCATATACGAAACGAGAGGGTATCGGATGAAATCAATTTCCCTGTA

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	96.80%	3.00%	0.15%	0.00%	NA
All Indica	2759	99.80%	0.00%	0.14%	0.00%	NA
All Japonica	1512	90.50%	9.30%	0.20%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.50%	0.00%	0.50%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.10%	0.13%	0.00%	NA
Temperate Japonica	767	81.70%	17.90%	0.39%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0802255218	G -> A	LOC_Os08g04540.1	upstream_gene_variant ; 789.0bp to feature; MODIFIER	silent_mutation	Average:56.907; most accessible tissue: Minghui63 root, score: 81.505	N	N	N	N
vg0802255218	G -> A	LOC_Os08g04530-LOC_Os08g04540	intergenic_region ; MODIFIER	silent_mutation	Average:56.907; most accessible tissue: Minghui63 root, score: 81.505	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0802255218	NA	2.37E-06	mr1062	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
vg0802255218	2.25E-06	2.51E-07	mr1425	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