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Detailed information for vg0609106483:

Variant ID: vg0609106483 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 9106483
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTGCTAATTACATGGGATCCGGGTATTATCTATCTGCTCGCTTGTGCCATGTTTACTTGATATTTGTCCTTTGTCAACCGGGGGTAATAAATCGACTAG[C/T]
TCATGTTACTTATGTAACCTAGCTAGAACTATATGCTTAGCCATGCTTAATTACCACTAGCTCAGTTGATGGGATAATTACAGTATTAGACCTTTTTAGT

Reverse complement sequence

ACTAAAAAGGTCTAATACTGTAATTATCCCATCAACTGAGCTAGTGGTAATTAAGCATGGCTAAGCATATAGTTCTAGCTAGGTTACATAAGTAACATGA[G/A]
CTAGTCGATTTATTACCCCCGGTTGACAAAGGACAAATATCAAGTAAACATGGCACAAGCGAGCAGATAGATAATACCCGGATCCCATGTAATTAGCAAA

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	33.90%	0.20%	4.30%	61.62%	NA
All Indica	2759	23.80%	0.30%	6.31%	69.63%	NA
All Japonica	1512	47.00%	0.00%	1.06%	51.98%	NA
Aus	269	69.90%	0.00%	1.86%	28.25%	NA
Indica I	595	15.30%	0.30%	4.87%	79.50%	NA
Indica II	465	16.30%	0.20%	6.45%	76.99%	NA
Indica III	913	33.20%	0.10%	8.00%	58.71%	NA
Indica Intermediate	786	23.70%	0.50%	5.34%	70.48%	NA
Temperate Japonica	767	74.20%	0.00%	0.65%	25.16%	NA
Tropical Japonica	504	19.20%	0.00%	1.19%	79.56%	NA
Japonica Intermediate	241	18.30%	0.00%	2.07%	79.67%	NA
VI/Aromatic	96	25.00%	0.00%	6.25%	68.75%	NA
Intermediate	90	27.80%	0.00%	2.22%	70.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0609106483	C -> T	LOC_Os06g16010.1	upstream_gene_variant ; 3364.0bp to feature; MODIFIER	silent_mutation	Average:13.316; most accessible tissue: Callus, score: 27.439	N	N	N	N
vg0609106483	C -> T	LOC_Os06g16000.1	downstream_gene_variant ; 4177.0bp to feature; MODIFIER	silent_mutation	Average:13.316; most accessible tissue: Callus, score: 27.439	N	N	N	N
vg0609106483	C -> T	LOC_Os06g16000-LOC_Os06g16010	intergenic_region ; MODIFIER	silent_mutation	Average:13.316; most accessible tissue: Callus, score: 27.439	N	N	N	N
vg0609106483	C -> DEL	N	N	silent_mutation	Average:13.316; most accessible tissue: Callus, score: 27.439	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0609106483	5.02E-06	NA	mr1566_2	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