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Detailed information for vg0225250931:

Variant ID: vg0225250931 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 25250931
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, G: 0.00, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:

ACCTCTACATATGCTTGCATTGACAAATAAAAATATTCTAAGTCCATTTGCACATGTAAACATTATCAGAAGTAAAAAAAAGTACTTTTCATAATTTTAC[T/G]
GTTTCACTGTAAGCTGCATTAAATGTGGCTTAGAAGCCAGGAAACACCCGTGTCTCATGAAGCAACGAATTTTACATGTCGCAAAACGTTGCATGGAATT

Reverse complement sequence

AATTCCATGCAACGTTTTGCGACATGTAAAATTCGTTGCTTCATGAGACACGGGTGTTTCCTGGCTTCTAAGCCACATTTAATGCAGCTTACAGTGAAAC[A/C]
GTAAAATTATGAAAAGTACTTTTTTTTACTTCTGATAATGTTTACATGTGCAAATGGACTTAGAATATTTTTATTTGTCAATGCAAGCATATGTAGAGGT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	86.20%	13.50%	0.08%	0.21%	NA
All Indica	2759	83.60%	16.00%	0.07%	0.29%	NA
All Japonica	1512	89.10%	10.70%	0.13%	0.07%	NA
Aus	269	96.30%	3.70%	0.00%	0.00%	NA
Indica I	595	78.20%	21.20%	0.00%	0.67%	NA
Indica II	465	77.00%	22.80%	0.00%	0.22%	NA
Indica III	913	93.80%	6.10%	0.00%	0.11%	NA
Indica Intermediate	786	79.90%	19.60%	0.25%	0.25%	NA
Temperate Japonica	767	96.20%	3.50%	0.13%	0.13%	NA
Tropical Japonica	504	80.40%	19.60%	0.00%	0.00%	NA
Japonica Intermediate	241	84.60%	14.90%	0.41%	0.00%	NA
VI/Aromatic	96	79.20%	20.80%	0.00%	0.00%	NA
Intermediate	90	93.30%	5.60%	0.00%	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
vg0225250931	T -> G	LOC_Os02g42020.3	downstream_gene_variant ; 78.0bp to feature; MODIFIER	silent_mutation	Average:59.426; most accessible tissue: Callus, score: 78.807	N	N	N	N
vg0225250931	T -> G	LOC_Os02g42020.1	intron_variant ; MODIFIER	silent_mutation	Average:59.426; most accessible tissue: Callus, score: 78.807	N	N	N	N
vg0225250931	T -> G	LOC_Os02g42020.2	intron_variant ; MODIFIER	silent_mutation	Average:59.426; most accessible tissue: Callus, score: 78.807	N	N	N	N
vg0225250931	T -> DEL	N	N	silent_mutation	Average:59.426; most accessible tissue: Callus, score: 78.807	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0225250931	NA	5.94E-06	mr1116	Jap_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
vg0225250931	NA	7.16E-06	mr1119	Jap_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
vg0225250931	NA	7.99E-06	mr1350	Jap_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
vg0225250931	NA	4.67E-07	mr1657	Jap_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
vg0225250931	NA	4.56E-07	mr1890	Jap_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
vg0225250931	1.78E-06	1.78E-06	mr1891	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
vg0225250931	NA	3.30E-06	mr1233_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
vg0225250931	NA	5.86E-06	mr1389_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