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Detailed information for vg0207032875:

Variant ID: vg0207032875 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 7032875
Reference Allele: G	Alternative Allele: T
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.71, T: 0.30, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

AATAAGGTTGTTATTATAACACAACTCACAAGGTTTGGAGAAAGTCCTGTTTTAAATGGTTTGGACAAACACACAAAAAACTTGTCAACATTCAAAACCA[G/T]
GAAGTCTTCCCTGTGCCTTTACCCACTAATGTTTACCAGAAACACCACTAAGATAGATAATGCAACTTTACTAGCCTGCTTAGTCATAGAGTTTTGCAGG

Reverse complement sequence

CCTGCAAAACTCTATGACTAAGCAGGCTAGTAAAGTTGCATTATCTATCTTAGTGGTGTTTCTGGTAAACATTAGTGGGTAAAGGCACAGGGAAGACTTC[C/A]
TGGTTTTGAATGTTGACAAGTTTTTTGTGTGTTTGTCCAAACCATTTAAAACAGGACTTTCTCCAAACCTTGTGAGTTGTGTTATAATAACAACCTTATT

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	55.20%	44.30%	0.21%	0.30%	NA
All Indica	2759	79.10%	20.10%	0.33%	0.43%	NA
All Japonica	1512	3.20%	96.80%	0.00%	0.00%	NA
Aus	269	97.80%	2.20%	0.00%	0.00%	NA
Indica I	595	71.80%	27.60%	0.00%	0.67%	NA
Indica II	465	89.00%	9.90%	0.22%	0.86%	NA
Indica III	913	80.70%	18.80%	0.22%	0.22%	NA
Indica Intermediate	786	77.00%	22.00%	0.76%	0.25%	NA
Temperate Japonica	767	2.10%	97.90%	0.00%	0.00%	NA
Tropical Japonica	504	4.00%	96.00%	0.00%	0.00%	NA
Japonica Intermediate	241	5.00%	95.00%	0.00%	0.00%	NA
VI/Aromatic	96	66.70%	33.30%	0.00%	0.00%	NA
Intermediate	90	55.60%	41.10%	1.11%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0207032875	G -> T	LOC_Os02g13190.1	upstream_gene_variant ; 4571.0bp to feature; MODIFIER	silent_mutation	Average:63.738; most accessible tissue: Minghui63 flower, score: 75.217	N	N	N	N
vg0207032875	G -> T	LOC_Os02g13200.1	intron_variant ; MODIFIER	silent_mutation	Average:63.738; most accessible tissue: Minghui63 flower, score: 75.217	N	N	N	N
vg0207032875	G -> DEL	N	N	silent_mutation	Average:63.738; most accessible tissue: Minghui63 flower, score: 75.217	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0207032875	NA	3.28E-17	mr1557	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
vg0207032875	NA	2.40E-18	mr1383_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