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Detailed information for vg0220169570:

Variant ID: vg0220169570 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 20169570
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.89, A: 0.10, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

GTAAGTAGCATCAACGTAATCTCTCAACCTACACTACAAAAAAAATCTAGAGCTGGGATCATGTAAAAGTAAAACTCAATCTGCCAATATGAAACTGAAA[G/A]
TATGAAGCCTGCGAAGAAATCATCCATCGCTGGTTAGTGTGAATGCTAGGAGAACACATGAGAGGGTGAAAACTATCATAGCAGAGGAGAAAGACAAGAT

Reverse complement sequence

ATCTTGTCTTTCTCCTCTGCTATGATAGTTTTCACCCTCTCATGTGTTCTCCTAGCATTCACACTAACCAGCGATGGATGATTTCTTCGCAGGCTTCATA[C/T]
TTTCAGTTTCATATTGGCAGATTGAGTTTTACTTTTACATGATCCCAGCTCTAGATTTTTTTTGTAGTGTAGGTTGAGAGATTACGTTGATGCTACTTAC

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	58.20%	41.40%	0.08%	0.25%	NA
All Indica	2759	91.20%	8.30%	0.11%	0.40%	NA
All Japonica	1512	1.80%	98.20%	0.00%	0.00%	NA
Aus	269	65.10%	34.90%	0.00%	0.00%	NA
Indica I	595	84.70%	14.60%	0.34%	0.34%	NA
Indica II	465	87.10%	12.70%	0.00%	0.22%	NA
Indica III	913	96.70%	3.10%	0.00%	0.22%	NA
Indica Intermediate	786	92.20%	6.90%	0.13%	0.76%	NA
Temperate Japonica	767	1.30%	98.70%	0.00%	0.00%	NA
Tropical Japonica	504	1.20%	98.80%	0.00%	0.00%	NA
Japonica Intermediate	241	4.60%	95.40%	0.00%	0.00%	NA
VI/Aromatic	96	2.10%	97.90%	0.00%	0.00%	NA
Intermediate	90	34.40%	63.30%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0220169570	G -> A	LOC_Os02g33820.1	upstream_gene_variant ; 2902.0bp to feature; MODIFIER	silent_mutation	Average:58.747; most accessible tissue: Zhenshan97 root, score: 77.09	N	N	N	N
vg0220169570	G -> A	LOC_Os02g33810.1	downstream_gene_variant ; 4961.0bp to feature; MODIFIER	silent_mutation	Average:58.747; most accessible tissue: Zhenshan97 root, score: 77.09	N	N	N	N
vg0220169570	G -> A	LOC_Os02g33830.1	downstream_gene_variant ; 20.0bp to feature; MODIFIER	silent_mutation	Average:58.747; most accessible tissue: Zhenshan97 root, score: 77.09	N	N	N	N
vg0220169570	G -> A	LOC_Os02g33820-LOC_Os02g33830	intergenic_region ; MODIFIER	silent_mutation	Average:58.747; most accessible tissue: Zhenshan97 root, score: 77.09	N	N	N	N
vg0220169570	G -> DEL	N	N	silent_mutation	Average:58.747; most accessible tissue: Zhenshan97 root, score: 77.09	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0220169570	6.10E-07	NA	mr1242_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