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Detailed information for vg0611149150:

Variant ID: vg0611149150 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 11149150
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.82, C: 0.18, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

CCAATTTTTGGTGTTAACAACAAGGTAAATATGTATTTGATGGGAAAATTGGTATGTTGCTCTCCGTTTATGTAGAACCAGCTAACAGATCAAGCATAAA[C/T]
AGGTGTCACATCCTGATTTTTGTTTCAGGATTTATAAATTATTTAATAAATTATTATTATAATTTATATTAAATGTTCATTAATTTACAAGTGAAGCTAA

Reverse complement sequence

TTAGCTTCACTTGTAAATTAATGAACATTTAATATAAATTATAATAATAATTTATTAAATAATTTATAAATCCTGAAACAAAAATCAGGATGTGACACCT[G/A]
TTTATGCTTGATCTGTTAGCTGGTTCTACATAAACGGAGAGCAACATACCAATTTTCCCATCAAATACATATTTACCTTGTTGTTAACACCAAAAATTGG

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	67.80%	8.70%	0.15%	23.30%	NA
All Indica	2759	61.00%	0.50%	0.18%	38.35%	NA
All Japonica	1512	72.00%	26.10%	0.07%	1.79%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	27.60%	0.50%	0.17%	71.76%	NA
Indica II	465	93.10%	0.00%	0.00%	6.88%	NA
Indica III	913	70.60%	0.20%	0.11%	29.03%	NA
Indica Intermediate	786	56.00%	1.10%	0.38%	42.49%	NA
Temperate Japonica	767	54.40%	43.40%	0.13%	2.09%	NA
Tropical Japonica	504	97.20%	2.20%	0.00%	0.60%	NA
Japonica Intermediate	241	75.50%	21.20%	0.00%	3.32%	NA
VI/Aromatic	96	92.70%	0.00%	0.00%	7.29%	NA
Intermediate	90	84.40%	4.40%	1.11%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0611149150	C -> T	LOC_Os06g19570.1	downstream_gene_variant ; 4255.0bp to feature; MODIFIER	silent_mutation	Average:19.286; most accessible tissue: Callus, score: 36.311	N	N	N	N
vg0611149150	C -> T	LOC_Os06g19570-LOC_Os06g19580	intergenic_region ; MODIFIER	silent_mutation	Average:19.286; most accessible tissue: Callus, score: 36.311	N	N	N	N
vg0611149150	C -> DEL	N	N	silent_mutation	Average:19.286; most accessible tissue: Callus, score: 36.311	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0611149150	NA	9.92E-07	mr1163	Jap_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
vg0611149150	5.00E-07	5.32E-09	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
vg0611149150	5.19E-06	3.78E-10	mr1570	Jap_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
vg0611149150	NA	1.84E-06	mr1063_2	Jap_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
vg0611149150	NA	4.30E-07	mr1096_2	Jap_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
vg0611149150	NA	1.21E-06	mr1161_2	Jap_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
vg0611149150	NA	5.01E-11	mr1570_2	Jap_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
vg0611149150	NA	7.81E-06	mr1617_2	Jap_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