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Detailed information for vg0305833332:

Variant ID: vg0305833332 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 5833332
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

CCTATACAGATCTTGCACCAGCCTCTGTGCATATTGAGTAAGAAGTCAATACATTTTGCATTTTCTTTAATAGAAATGGTAAAACACAGATCATGTTTTA[C/T]
CTACAAATAGAAGCACAGGAATCAAGTAAATTACCATAGAATCACCCCCCTGCCTACCAAGGAAACTAGGCCCTATTCGCCTCCCCAAGCAATCTGCAAA

Reverse complement sequence

TTTGCAGATTGCTTGGGGAGGCGAATAGGGCCTAGTTTCCTTGGTAGGCAGGGGGGTGATTCTATGGTAATTTACTTGATTCCTGTGCTTCTATTTGTAG[G/A]
TAAAACATGATCTGTGTTTTACCATTTCTATTAAAGAAAATGCAAAATGTATTGACTTCTTACTCAATATGCACAGAGGCTGGTGCAAGATCTGTATAGG

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	78.20%	21.40%	0.08%	0.30%	NA
All Indica	2759	65.50%	33.80%	0.14%	0.51%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	85.90%	14.10%	0.00%	0.00%	NA
Indica I	595	47.20%	51.60%	0.50%	0.67%	NA
Indica II	465	43.00%	56.10%	0.00%	0.86%	NA
Indica III	913	89.70%	10.10%	0.00%	0.22%	NA
Indica Intermediate	786	64.60%	34.70%	0.13%	0.51%	NA
Temperate Japonica	767	99.20%	0.80%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	81.20%	18.80%	0.00%	0.00%	NA
Intermediate	90	83.30%	16.70%	0.00%	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
vg0305833332	C -> T	LOC_Os03g11335.1	upstream_gene_variant ; 3018.0bp to feature; MODIFIER	silent_mutation	Average:33.77; most accessible tissue: Callus, score: 56.87	N	N	N	N
vg0305833332	C -> T	LOC_Os03g11330.1	intron_variant ; MODIFIER	silent_mutation	Average:33.77; most accessible tissue: Callus, score: 56.87	N	N	N	N
vg0305833332	C -> DEL	N	N	silent_mutation	Average:33.77; most accessible tissue: Callus, score: 56.87	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0305833332	NA	2.34E-06	mr1559_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
vg0305833332	3.96E-06	NA	mr1878_2	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
vg0305833332	NA	1.25E-06	mr1878_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