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Detailed information for vg0220063050:

Variant ID: vg0220063050 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 20063050
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATCCCATGTACTTTCTTTGTCTCAAAATATAAAGGATTTTGGTTAAATATAACACATCATAGTACTACGAACTTGGACAAACTATTTATCCAAATTCATA[G/A]
TACTAAAATGTGTCAGTTCTGATAAAAAAAATTTATATATTTTTTGAAACGGAAGGAGTAAACTCTTGACATTTTAGGATTGAAACTTAGGATATGTATC

Reverse complement sequence

GATACATATCCTAAGTTTCAATCCTAAAATGTCAAGAGTTTACTCCTTCCGTTTCAAAAAATATATAAATTTTTTTTATCAGAACTGACACATTTTAGTA[C/T]
TATGAATTTGGATAAATAGTTTGTCCAAGTTCGTAGTACTATGATGTGTTATATTTAACCAAAATCCTTTATATTTTGAGACAAAGAAAGTACATGGGAT

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	97.30%	2.20%	0.49%	0.00%	NA
All Indica	2759	99.00%	0.80%	0.18%	0.00%	NA
All Japonica	1512	93.60%	5.20%	1.19%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.70%	0.00%	0.34%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	97.40%	2.30%	0.33%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	88.30%	9.50%	2.22%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	97.50%	2.50%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	3.30%	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
vg0220063050	G -> A	LOC_Os02g33670-LOC_Os02g33680	intergenic_region ; MODIFIER	silent_mutation	Average:58.224; most accessible tissue: Callus, score: 91.181	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0220063050	2.09E-06	6.74E-08	mr1654	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