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Detailed information for vg0609106093:

Variant ID: vg0609106093 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 9106093
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTCAGCAACCCTCTTTTCCTTTGGAAAAATAAATGATAATTGCGTCATAATTCGTTAATAATTATAGAAATCCATTAAAATGGCTCAAAACTTCTAAAAT[C/T]
CATATCTAATTCATTCGAACTCCAAATTGAGCCATTCAACTTGCAAAATTCATCTAAAATTGAGCTCTACATGTTTGTTTACTTTTGATGTATTGTTTTC

Reverse complement sequence

GAAAACAATACATCAAAAGTAAACAAACATGTAGAGCTCAATTTTAGATGAATTTTGCAAGTTGAATGGCTCAATTTGGAGTTCGAATGAATTAGATATG[G/A]
ATTTTAGAAGTTTTGAGCCATTTTAATGGATTTCTATAATTATTAACGAATTATGACGCAATTATCATTTATTTTTCCAAAGGAAAAGAGGGTTGCTGAC

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	16.10%	1.10%	6.58%	76.22%	NA
All Indica	2759	2.90%	1.60%	3.15%	92.28%	NA
All Japonica	1512	39.40%	0.10%	2.05%	58.47%	NA
Aus	269	23.00%	3.00%	66.91%	7.06%	NA
Indica I	595	1.50%	0.20%	1.51%	96.81%	NA
Indica II	465	2.60%	6.20%	5.38%	85.81%	NA
Indica III	913	3.20%	0.30%	2.96%	93.54%	NA
Indica Intermediate	786	3.90%	1.50%	3.31%	91.22%	NA
Temperate Japonica	767	72.10%	0.00%	0.52%	27.38%	NA
Tropical Japonica	504	2.20%	0.00%	1.98%	95.83%	NA
Japonica Intermediate	241	13.30%	0.40%	7.05%	79.25%	NA
VI/Aromatic	96	11.50%	0.00%	10.42%	78.12%	NA
Intermediate	90	10.00%	0.00%	3.33%	86.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0609106093	C -> T	LOC_Os06g16010.1	upstream_gene_variant ; 3754.0bp to feature; MODIFIER	silent_mutation	Average:7.271; most accessible tissue: Zhenshan97 root, score: 10.511	N	N	N	N
vg0609106093	C -> T	LOC_Os06g16000.1	downstream_gene_variant ; 3787.0bp to feature; MODIFIER	silent_mutation	Average:7.271; most accessible tissue: Zhenshan97 root, score: 10.511	N	N	N	N
vg0609106093	C -> T	LOC_Os06g16000-LOC_Os06g16010	intergenic_region ; MODIFIER	silent_mutation	Average:7.271; most accessible tissue: Zhenshan97 root, score: 10.511	N	N	N	N
vg0609106093	C -> DEL	N	N	silent_mutation	Average:7.271; most accessible tissue: Zhenshan97 root, score: 10.511	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0609106093	2.72E-06	2.72E-06	mr1445	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