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Detailed information for vg0208276077:

Variant ID: vg0208276077 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 8276077
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.09, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

CAAAAGTGATTGTCTAAGTTTTAACTTTTGACTAAATCTTGTTTTACGTATCAAAATATTTATAAACAGATGAAGTACCGCATATAACTTATTGCCTTGA[C/T]
AAATAAAAACTCCATGGACACCCAGACCAACCACCGTGTGGGTGGCTACACGCCCGGAGAAGGCCTGTTGAGAGAGTGTGGCTAGAGCGAAGGTAGTGCA

Reverse complement sequence

TGCACTACCTTCGCTCTAGCCACACTCTCTCAACAGGCCTTCTCCGGGCGTGTAGCCACCCACACGGTGGTTGGTCTGGGTGTCCATGGAGTTTTTATTT[G/A]
TCAAGGCAATAAGTTATATGCGGTACTTCATCTGTTTATAAATATTTTGATACGTAAAACAAGATTTAGTCAAAAGTTAAAACTTAGACAATCACTTTTG

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	66.40%	11.40%	0.70%	21.48%	NA
All Indica	2759	59.30%	18.30%	0.76%	21.57%	NA
All Japonica	1512	73.30%	1.10%	0.79%	24.80%	NA
Aus	269	98.90%	0.70%	0.00%	0.37%	NA
Indica I	595	25.50%	34.80%	1.51%	38.15%	NA
Indica II	465	65.80%	27.10%	0.22%	6.88%	NA
Indica III	913	78.10%	3.60%	0.11%	18.18%	NA
Indica Intermediate	786	59.30%	17.80%	1.27%	21.63%	NA
Temperate Japonica	767	94.70%	1.60%	0.00%	3.78%	NA
Tropical Japonica	504	41.50%	0.20%	2.18%	56.15%	NA
Japonica Intermediate	241	71.80%	1.70%	0.41%	26.14%	NA
VI/Aromatic	96	65.60%	1.00%	0.00%	33.33%	NA
Intermediate	90	72.20%	14.40%	0.00%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0208276077	C -> T	LOC_Os02g14874.1	upstream_gene_variant ; 729.0bp to feature; MODIFIER	silent_mutation	Average:42.76; most accessible tissue: Minghui63 root, score: 74.812	N	N	N	N
vg0208276077	C -> T	LOC_Os02g14874.2	upstream_gene_variant ; 766.0bp to feature; MODIFIER	silent_mutation	Average:42.76; most accessible tissue: Minghui63 root, score: 74.812	N	N	N	N
vg0208276077	C -> T	LOC_Os02g14870-LOC_Os02g14874	intergenic_region ; MODIFIER	silent_mutation	Average:42.76; most accessible tissue: Minghui63 root, score: 74.812	N	N	N	N
vg0208276077	C -> DEL	N	N	silent_mutation	Average:42.76; most accessible tissue: Minghui63 root, score: 74.812	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0208276077	9.94E-07	9.94E-07	mr1747	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
vg0208276077	NA	9.56E-07	mr1909	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