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Detailed information for vg0228079496:

Variant ID: vg0228079496 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 28079496
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 322. )

Flanking Sequence (100 bp) in Reference Genome:

TCAAAGCTGTGTTTACTAGCCTCTTTGCAATTCCCTACCAAAATTATGGAAATTAGATTTAGCACCTTTCCAAGTAATCAGCCTAGGCATTGCGGGATAG[T/C]
CCCACAAACAAAGAAAAACAAGCAACGACACATGTAAGTAAAGGTCTGAAGACATACTGCTCGTGGATTTTTGTAGACGATGTCAACAGCTTGTTGGTTT

Reverse complement sequence

AAACCAACAAGCTGTTGACATCGTCTACAAAAATCCACGAGCAGTATGTCTTCAGACCTTTACTTACATGTGTCGTTGCTTGTTTTTCTTTGTTTGTGGG[A/G]
CTATCCCGCAATGCCTAGGCTGATTACTTGGAAAGGTGCTAAATCTAATTTCCATAATTTTGGTAGGGAATTGCAAAGAGGCTAGTAAACACAGCTTTGA

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	59.90%	39.80%	0.28%	0.06%	NA
All Indica	2759	94.90%	4.60%	0.36%	0.11%	NA
All Japonica	1512	0.60%	99.40%	0.00%	0.00%	NA
Aus	269	62.10%	37.50%	0.37%	0.00%	NA
Indica I	595	98.20%	1.20%	0.50%	0.17%	NA
Indica II	465	97.40%	2.20%	0.43%	0.00%	NA
Indica III	913	91.30%	8.30%	0.22%	0.11%	NA
Indica Intermediate	786	95.00%	4.50%	0.38%	0.13%	NA
Temperate Japonica	767	0.30%	99.70%	0.00%	0.00%	NA
Tropical Japonica	504	1.20%	98.80%	0.00%	0.00%	NA
Japonica Intermediate	241	0.40%	99.60%	0.00%	0.00%	NA
VI/Aromatic	96	1.00%	99.00%	0.00%	0.00%	NA
Intermediate	90	37.80%	60.00%	2.22%	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
vg0228079496	T -> DEL	N	N	silent_mutation	Average:54.23; most accessible tissue: Callus, score: 82.378	N	N	N	N
vg0228079496	T -> C	LOC_Os02g46070.1	downstream_gene_variant ; 4194.0bp to feature; MODIFIER	silent_mutation	Average:54.23; most accessible tissue: Callus, score: 82.378	N	N	N	N
vg0228079496	T -> C	LOC_Os02g46080.1	intron_variant ; MODIFIER	silent_mutation	Average:54.23; most accessible tissue: Callus, score: 82.378	N	N	N	N
vg0228079496	T -> C	LOC_Os02g46080.2	intron_variant ; MODIFIER	silent_mutation	Average:54.23; most accessible tissue: Callus, score: 82.378	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0228079496	4.28E-06	1.82E-81	mr1629	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
vg0228079496	NA	1.02E-09	mr1905	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
vg0228079496	7.45E-06	NA	mr1629_2	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