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Detailed information for vg0220225964:

Variant ID: vg0220225964 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 20225964
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 345. )

Flanking Sequence (100 bp) in Reference Genome:

TATCCTAAAATTAATCGATAAATAGCATTGCCGTACTTTCTTCAAACTCAGTCTCCTTTCAACATTCACCACTATCTTTTCCAGAACCAAGTCCGACAAA[G/T]
AGTGAGCTTTCAGCCATCATCCATCCCTCGTCGTCTAACTCTATCATCTCGCAGCCGATGCATTCCATCCGATATAGACCCATCAGCCTCAGCTGATACA

Reverse complement sequence

TGTATCAGCTGAGGCTGATGGGTCTATATCGGATGGAATGCATCGGCTGCGAGATGATAGAGTTAGACGACGAGGGATGGATGATGGCTGAAAGCTCACT[C/A]
TTTGTCGGACTTGGTTCTGGAAAAGATAGTGGTGAATGTTGAAAGGAGACTGAGTTTGAAGAAAGTACGGCAATGCTATTTATCGATTAATTTTAGGATA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	95.20%	2.70%	1.74%	0.32%	NA
All Indica	2759	92.40%	4.20%	2.79%	0.54%	NA
All Japonica	1512	99.40%	0.50%	0.13%	0.00%	NA
Aus	269	98.90%	0.00%	1.12%	0.00%	NA
Indica I	595	86.20%	7.20%	4.87%	1.68%	NA
Indica II	465	90.30%	5.60%	4.09%	0.00%	NA
Indica III	913	99.70%	0.10%	0.22%	0.00%	NA
Indica Intermediate	786	89.90%	6.00%	3.44%	0.64%	NA
Temperate Japonica	767	99.50%	0.40%	0.13%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	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
vg0220225964	G -> T	LOC_Os02g33930.1	upstream_gene_variant ; 1550.0bp to feature; MODIFIER	silent_mutation	Average:58.648; most accessible tissue: Zhenshan97 young leaf, score: 90.27	N	N	N	N
vg0220225964	G -> T	LOC_Os02g33944.1	upstream_gene_variant ; 1062.0bp to feature; MODIFIER	silent_mutation	Average:58.648; most accessible tissue: Zhenshan97 young leaf, score: 90.27	N	N	N	N
vg0220225964	G -> T	LOC_Os02g33930-LOC_Os02g33944	intergenic_region ; MODIFIER	silent_mutation	Average:58.648; most accessible tissue: Zhenshan97 young leaf, score: 90.27	N	N	N	N
vg0220225964	G -> DEL	N	N	silent_mutation	Average:58.648; most accessible tissue: Zhenshan97 young leaf, score: 90.27	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0220225964	NA	1.37E-06	mr1038_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
vg0220225964	NA	6.14E-07	mr1038_2	Ind_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
vg0220225964	1.29E-06	NA	mr1717_2	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
vg0220225964	3.13E-07	NA	mr1770_2	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
vg0220225964	8.79E-07	NA	mr1946_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
vg0220225964	8.79E-07	NA	mr1948_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