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Detailed information for vg0223273272:

Variant ID: vg0223273272 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 23273272
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:

AGTTAACATGGCTGTCATGTTTTGGGTCAGGCCCCATGGGCTTGTGTGATGTTTAGTTTCTTTACTTGCTCTGAACCTTTTGTAAGAATCTTATCATTTC[G/A]
TTAATGAAATGGGAGGGTCTCCGCTCTCTGTCTCAAAAAAAAAAAATCATGGAAGGGGTCTGTGATAAAAAAAAAGGAGGTCTTGAGTTTTTGTTTTGAC

Reverse complement sequence

GTCAAAACAAAAACTCAAGACCTCCTTTTTTTTTATCACAGACCCCTTCCATGATTTTTTTTTTTTGAGACAGAGAGCGGAGACCCTCCCATTTCATTAA[C/T]
GAAATGATAAGATTCTTACAAAAGGTTCAGAGCAAGTAAAGAAACTAAACATCACACAAGCCCATGGGGCCTGACCCAAAACATGACAGCCATGTTAACT

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	89.10%	10.50%	0.47%	0.00%	NA
All Indica	2759	82.20%	17.20%	0.62%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.07%	0.00%	NA
Aus	269	92.60%	5.90%	1.49%	0.00%	NA
Indica I	595	70.40%	27.90%	1.68%	0.00%	NA
Indica II	465	95.90%	3.90%	0.22%	0.00%	NA
Indica III	913	76.50%	23.30%	0.22%	0.00%	NA
Indica Intermediate	786	89.70%	9.80%	0.51%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.20%	0.20%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	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
vg0223273272	G -> A	LOC_Os02g38490.1	3_prime_UTR_variant ; 136.0bp to feature; MODIFIER	silent_mutation	Average:51.61; most accessible tissue: Callus, score: 66.394	N	N	N	N
vg0223273272	G -> A	LOC_Os02g38490.2	3_prime_UTR_variant ; 210.0bp to feature; MODIFIER	silent_mutation	Average:51.61; most accessible tissue: Callus, score: 66.394	N	N	N	N
vg0223273272	G -> A	LOC_Os02g38490.3	3_prime_UTR_variant ; 303.0bp to feature; MODIFIER	silent_mutation	Average:51.61; most accessible tissue: Callus, score: 66.394	N	N	N	N
vg0223273272	G -> A	LOC_Os02g38480.1	downstream_gene_variant ; 1322.0bp to feature; MODIFIER	silent_mutation	Average:51.61; most accessible tissue: Callus, score: 66.394	N	N	N	N
vg0223273272	G -> A	LOC_Os02g38490.4	intron_variant ; MODIFIER	silent_mutation	Average:51.61; most accessible tissue: Callus, score: 66.394	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0223273272	NA	2.71E-06	mr1069	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
vg0223273272	NA	2.30E-06	mr1149	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
vg0223273272	NA	2.34E-06	mr1441	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
vg0223273272	NA	4.03E-06	mr1929	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
vg0223273272	4.78E-06	NA	mr1149_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
vg0223273272	NA	4.87E-09	mr1149_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
vg0223273272	NA	6.54E-09	mr1441_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