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Detailed information for vg0208101334:

Variant ID: vg0208101334 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 8101334
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCTCCCAGAGCCATTTCACTTGATTAATCGGCTCCCAGAGCCTTTTTCATTTTCTCGGACTCCCAGAGTCCAGCTGCCCAGCAGCACAACAATCCGCTTC[T/C]
ACTCGGGAAGCCTAGTCTATGATGCCCATAGACATCCCGAATCACACAGATTTGTTTCTTGACCACTCAGGTCATCCATCTGCCACATAGGCTGATTCTG

Reverse complement sequence

CAGAATCAGCCTATGTGGCAGATGGATGACCTGAGTGGTCAAGAAACAAATCTGTGTGATTCGGGATGTCTATGGGCATCATAGACTAGGCTTCCCGAGT[A/G]
GAAGCGGATTGTTGTGCTGCTGGGCAGCTGGACTCTGGGAGTCCGAGAAAATGAAAAAGGCTCTGGGAGCCGATTAATCAAGTGAAATGGCTCTGGGAGC

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	51.10%	0.80%	15.32%	32.82%	NA
All Indica	2759	30.20%	1.40%	14.79%	53.64%	NA
All Japonica	1512	98.00%	0.00%	0.53%	1.46%	NA
Aus	269	3.70%	0.00%	92.19%	4.09%	NA
Indica I	595	35.80%	0.00%	5.04%	59.16%	NA
Indica II	465	16.10%	0.40%	12.90%	70.54%	NA
Indica III	913	34.90%	2.70%	21.47%	40.85%	NA
Indica Intermediate	786	28.80%	1.40%	15.52%	54.33%	NA
Temperate Japonica	767	98.40%	0.00%	0.26%	1.30%	NA
Tropical Japonica	504	97.80%	0.00%	0.60%	1.59%	NA
Japonica Intermediate	241	97.10%	0.00%	1.24%	1.66%	NA
VI/Aromatic	96	43.80%	0.00%	46.88%	9.38%	NA
Intermediate	90	51.10%	0.00%	16.67%	32.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0208101334	T -> DEL	N	N	silent_mutation	Average:24.785; most accessible tissue: Zhenshan97 flag leaf, score: 56.01	N	N	N	N
vg0208101334	T -> C	LOC_Os02g14680-LOC_Os02g14700	intergenic_region ; MODIFIER	silent_mutation	Average:24.785; most accessible tissue: Zhenshan97 flag leaf, score: 56.01	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0208101334	8.70E-07	4.91E-06	mr1928	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
vg0208101334	4.26E-06	3.59E-06	mr1928	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