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Detailed information for vg0214609392:

Variant ID: vg0214609392 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 14609392
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGTATTACTTCTTGATTAAGAAGGCCTGAACCTGTATAAAATTCCTTTTCTCTAAACCCATCCACTTTTCTAGCTTGATAGCCACCCCCTTTTAGTATTG[C/T]
CGAAATCTTGTTTCGACAGGCAGTGATGGTGGGCTCAGGAGACGACGGGAGGGGCCTCCAAACGCACAGATCCCACCACCTCTCTCCCTCATCATCTTCG

Reverse complement sequence

CGAAGATGATGAGGGAGAGAGGTGGTGGGATCTGTGCGTTTGGAGGCCCCTCCCGTCGTCTCCTGAGCCCACCATCACTGCCTGTCGAAACAAGATTTCG[G/A]
CAATACTAAAAGGGGGTGGCTATCAAGCTAGAAAAGTGGATGGGTTTAGAGAAAAGGAATTTTATACAGGTTCAGGCCTTCTTAATCAAGAAGTAATACC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	62.30%	37.70%	0.02%	0.00%	NA
All Indica	2759	96.70%	3.30%	0.04%	0.00%	NA
All Japonica	1512	1.60%	98.40%	0.00%	0.00%	NA
Aus	269	75.10%	24.90%	0.00%	0.00%	NA
Indica I	595	99.20%	0.80%	0.00%	0.00%	NA
Indica II	465	96.10%	3.90%	0.00%	0.00%	NA
Indica III	913	97.30%	2.70%	0.00%	0.00%	NA
Indica Intermediate	786	94.40%	5.50%	0.13%	0.00%	NA
Temperate Japonica	767	0.80%	99.20%	0.00%	0.00%	NA
Tropical Japonica	504	2.40%	97.60%	0.00%	0.00%	NA
Japonica Intermediate	241	2.50%	97.50%	0.00%	0.00%	NA
VI/Aromatic	96	9.40%	90.60%	0.00%	0.00%	NA
Intermediate	90	44.40%	55.60%	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
vg0214609392	C -> T	LOC_Os02g25140.1	upstream_gene_variant ; 2280.0bp to feature; MODIFIER	silent_mutation	Average:48.077; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N
vg0214609392	C -> T	LOC_Os02g25150.1	upstream_gene_variant ; 2717.0bp to feature; MODIFIER	silent_mutation	Average:48.077; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N
vg0214609392	C -> T	LOC_Os02g25140-LOC_Os02g25150	intergenic_region ; MODIFIER	silent_mutation	Average:48.077; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0214609392	1.08E-06	1.42E-06	mr1125	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
vg0214609392	2.92E-06	8.79E-06	mr1140	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
vg0214609392	8.11E-08	4.54E-07	mr1758	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