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Detailed information for vg0608359756:

Variant ID: vg0608359756 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 8359756
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AACCTATAGAAAGAGAGCATTCCATTTTCTTTGTATGATTTTAATTTTTGGGTTTGCGCTTTTGTATTTGAGTCTCTATTTTTTTTATTTATATTTGAGT[C/T]
ACCGTAATCTTGCAATAAGGTACTTGAGGTTGTTTTTGTTAAAAAAAATCAAAAGAAAGGAGAGAACCAAGGCAGAAAGGTGCATAAAAAGAAAAAGAAA

Reverse complement sequence

TTTCTTTTTCTTTTTATGCACCTTTCTGCCTTGGTTCTCTCCTTTCTTTTGATTTTTTTTAACAAAAACAACCTCAAGTACCTTATTGCAAGATTACGGT[G/A]
ACTCAAATATAAATAAAAAAAATAGAGACTCAAATACAAAAGCGCAAACCCAAAAATTAAAATCATACAAAGAAAATGGAATGCTCTCTTTCTATAGGTT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	94.80%	4.60%	0.57%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	88.00%	10.30%	1.65%	0.00%	NA
Aus	269	98.50%	1.10%	0.37%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	96.60%	2.10%	1.30%	0.00%	NA
Tropical Japonica	504	85.50%	13.10%	1.39%	0.00%	NA
Japonica Intermediate	241	66.00%	30.70%	3.32%	0.00%	NA
VI/Aromatic	96	47.90%	52.10%	0.00%	0.00%	NA
Intermediate	90	92.20%	6.70%	1.11%	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
vg0608359756	C -> T	LOC_Os06g14750-LOC_Os06g14770	intergenic_region ; MODIFIER	silent_mutation	Average:31.576; most accessible tissue: Callus, score: 50.897	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0608359756	6.26E-07	6.26E-07	mr1526	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
vg0608359756	NA	1.72E-09	mr1057_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