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Detailed information for vg0620360503:

Variant ID: vg0620360503 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 20360503
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATCAACTAAAATATAGTGATTACTTTGGTGAGTTATAAGCACTAAAGTAAATATTAATTGCTTAGACATGGTGTTTAGGTAGTTGTTATCCAGTAATTGC[T/A]
GTGTATCCCACAGTACGTTTGAGGTAGGTGTAGAGGTGGTGACAGCCCTCAAGATCACTTATGTCCTCCCTGTCCGGGTACGTAGTAGAGCGACAACTAG

Reverse complement sequence

CTAGTTGTCGCTCTACTACGTACCCGGACAGGGAGGACATAAGTGATCTTGAGGGCTGTCACCACCTCTACACCTACCTCAAACGTACTGTGGGATACAC[A/T]
GCAATTACTGGATAACAACTACCTAAACACCATGTCTAAGCAATTAATATTTACTTTAGTGCTTATAACTCACCAAAGTAATCACTATATTTTAGTTGAT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	36.20%	1.00%	12.59%	50.19%	NA
All Indica	2759	6.90%	1.80%	16.75%	74.59%	NA
All Japonica	1512	92.00%	0.00%	0.40%	7.61%	NA
Aus	269	15.60%	0.00%	37.55%	46.84%	NA
Indica I	595	5.20%	1.00%	13.95%	79.83%	NA
Indica II	465	8.20%	2.40%	12.69%	76.77%	NA
Indica III	913	5.70%	1.80%	19.17%	73.38%	NA
Indica Intermediate	786	8.80%	2.00%	18.45%	70.74%	NA
Temperate Japonica	767	92.80%	0.00%	0.26%	6.91%	NA
Tropical Japonica	504	93.30%	0.00%	0.79%	5.95%	NA
Japonica Intermediate	241	86.70%	0.00%	0.00%	13.28%	NA
VI/Aromatic	96	41.70%	0.00%	18.75%	39.58%	NA
Intermediate	90	52.20%	0.00%	8.89%	38.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0620360503	T -> A	LOC_Os06g35020.1	upstream_gene_variant ; 4568.0bp to feature; MODIFIER	silent_mutation	Average:14.031; most accessible tissue: Callus, score: 38.196	N	N	N	N
vg0620360503	T -> A	LOC_Os06g35010.1	downstream_gene_variant ; 395.0bp to feature; MODIFIER	silent_mutation	Average:14.031; most accessible tissue: Callus, score: 38.196	N	N	N	N
vg0620360503	T -> A	LOC_Os06g35000-LOC_Os06g35010	intergenic_region ; MODIFIER	silent_mutation	Average:14.031; most accessible tissue: Callus, score: 38.196	N	N	N	N
vg0620360503	T -> DEL	N	N	silent_mutation	Average:14.031; most accessible tissue: Callus, score: 38.196	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0620360503	2.69E-06	NA	mr1874	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