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Detailed information for vg0609055058:

Variant ID: vg0609055058 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 9055058
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.95, C: 0.05, others allele: 0.00, population size: 81. )

Flanking Sequence (100 bp) in Reference Genome:

GTGACTCGAGCAATGTCCGCCCGAAAAAAGCCATGACAAATGGAAGCGGCGGCTTCTTCGGAGGTAAGGTGTCCTTGTGTTCACAATTGCACAGATGGCG[T/C]
GAAATTGTAAGGTGGGCGGCCATACGGAACCCATGTGGTATATATGTGATCTCTGAGTTAGGTTTTTTTTTCTTTTCTTTTTTAGGGGGGGTGGGGGGGG

Reverse complement sequence

CCCCCCCCACCCCCCCTAAAAAAGAAAAGAAAAAAAAACCTAACTCAGAGATCACATATATACCACATGGGTTCCGTATGGCCGCCCACCTTACAATTTC[A/G]
CGCCATCTGTGCAATTGTGAACACAAGGACACCTTACCTCCGAAGAAGCCGCCGCTTCCATTTGTCATGGCTTTTTTCGGGCGGACATTGCTCGAGTCAC

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	76.10%	21.60%	1.54%	0.76%	NA
All Indica	2759	69.00%	27.10%	2.57%	1.30%	NA
All Japonica	1512	99.70%	0.20%	0.07%	0.00%	NA
Aus	269	8.60%	91.40%	0.00%	0.00%	NA
Indica I	595	60.30%	33.90%	4.20%	1.51%	NA
Indica II	465	94.60%	4.90%	0.43%	0.00%	NA
Indica III	913	56.30%	37.60%	3.50%	2.63%	NA
Indica Intermediate	786	75.10%	23.00%	1.53%	0.38%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.40%	0.41%	0.00%	NA
VI/Aromatic	96	91.70%	8.30%	0.00%	0.00%	NA
Intermediate	90	82.20%	16.70%	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
vg0609055058	T -> C	LOC_Os06g15920.1	upstream_gene_variant ; 3097.0bp to feature; MODIFIER	silent_mutation	Average:68.42; most accessible tissue: Callus, score: 96.759	N	N	N	N
vg0609055058	T -> C	LOC_Os06g15910-LOC_Os06g15920	intergenic_region ; MODIFIER	silent_mutation	Average:68.42; most accessible tissue: Callus, score: 96.759	N	N	N	N
vg0609055058	T -> DEL	N	N	silent_mutation	Average:68.42; most accessible tissue: Callus, score: 96.759	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0609055058	2.85E-07	NA	mr1570	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
vg0609055058	3.02E-08	2.57E-11	mr1570	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
vg0609055058	NA	1.15E-09	mr1607	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
vg0609055058	4.70E-07	6.36E-11	mr1570_2	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