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Detailed information for vg0114890522:

Variant ID: vg0114890522 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 14890522
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.94, G: 0.06, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:

GTACCCCGTTTAATATTATAAGTCATTTAAGTTTTTTTTAGTACTATTTTCAACATAAAACAAATATATCATTAAACTATATCCAAGGTTAGATTTAATG[G/A]
AACTAATTTCATATTTTAGATGTTAATTTTTTCGATAAACTCGGTTAAAGTTTGACAAAAAAAAAAGTAAAACGACTTATAATATAAAACGGAGGTATTA

Reverse complement sequence

TAATACCTCCGTTTTATATTATAAGTCGTTTTACTTTTTTTTTTGTCAAACTTTAACCGAGTTTATCGAAAAAATTAACATCTAAAATATGAAATTAGTT[C/T]
CATTAAATCTAACCTTGGATATAGTTTAATGATATATTTGTTTTATGTTGAAAATAGTACTAAAAAAAACTTAAATGACTTATAATATTAAACGGGGTAC

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	48.80%	35.30%	0.08%	15.76%	NA
All Indica	2759	75.30%	6.70%	0.11%	17.87%	NA
All Japonica	1512	0.50%	87.00%	0.07%	12.43%	NA
Aus	269	45.70%	33.80%	0.00%	20.45%	NA
Indica I	595	67.40%	15.80%	0.17%	16.64%	NA
Indica II	465	83.00%	5.20%	0.00%	11.83%	NA
Indica III	913	73.10%	1.50%	0.00%	25.41%	NA
Indica Intermediate	786	79.40%	6.70%	0.25%	13.61%	NA
Temperate Japonica	767	0.40%	94.40%	0.00%	5.22%	NA
Tropical Japonica	504	0.20%	91.50%	0.00%	8.33%	NA
Japonica Intermediate	241	1.20%	54.40%	0.41%	43.98%	NA
VI/Aromatic	96	59.40%	38.50%	0.00%	2.08%	NA
Intermediate	90	46.70%	45.60%	0.00%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0114890522	G -> A	LOC_Os01g26270.1	upstream_gene_variant ; 2354.0bp to feature; MODIFIER	silent_mutation	Average:19.226; most accessible tissue: Callus, score: 56.034	N	N	N	N
vg0114890522	G -> A	LOC_Os01g26250-LOC_Os01g26270	intergenic_region ; MODIFIER	silent_mutation	Average:19.226; most accessible tissue: Callus, score: 56.034	N	N	N	N
vg0114890522	G -> DEL	N	N	silent_mutation	Average:19.226; most accessible tissue: Callus, score: 56.034	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0114890522	NA	9.54E-09	mr1198_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
vg0114890522	8.10E-06	NA	mr1383_2	Ind_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