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Detailed information for vg0335310058:

Variant ID: vg0335310058 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 35310058
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.94, T: 0.06, others allele: 0.00, population size: 65. )

Flanking Sequence (100 bp) in Reference Genome:

CTATTCTATGAATTTAGACACGTAAAGCACATATATACATCAAAACAGCCGAAATTCTGACAAATCGACCTTTAATAAAATTTATTTTGAAAATAGACCC[A/T]
AAATATTCCTTACTTCCCTAAATGTTTGACGCTGTTGACTTTTTAAAGTATGTTTAACCATTTGTCTTATTCAAAAACTTTTGTGAAATATGTAAAACTA

Reverse complement sequence

TAGTTTTACATATTTCACAAAAGTTTTTGAATAAGACAAATGGTTAAACATACTTTAAAAAGTCAACAGCGTCAAACATTTAGGGAAGTAAGGAATATTT[T/A]
GGGTCTATTTTCAAAATAAATTTTATTAAAGGTCGATTTGTCAGAATTTCGGCTGTTTTGATGTATATATGTGCTTTACGTGTCTAAATTCATAGAATAG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	70.60%	29.40%	0.06%	0.00%	NA
All Indica	2759	59.50%	40.40%	0.07%	0.00%	NA
All Japonica	1512	98.30%	1.70%	0.00%	0.00%	NA
Aus	269	19.30%	80.70%	0.00%	0.00%	NA
Indica I	595	73.80%	26.20%	0.00%	0.00%	NA
Indica II	465	36.30%	63.70%	0.00%	0.00%	NA
Indica III	913	67.90%	32.00%	0.11%	0.00%	NA
Indica Intermediate	786	52.50%	47.30%	0.13%	0.00%	NA
Temperate Japonica	767	99.50%	0.50%	0.00%	0.00%	NA
Tropical Japonica	504	96.00%	4.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	67.80%	31.10%	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
vg0335310058	A -> T	LOC_Os03g62330.1	3_prime_UTR_variant ; 251.0bp to feature; MODIFIER	silent_mutation	Average:59.753; most accessible tissue: Minghui63 root, score: 78.091	N	N	N	N
vg0335310058	A -> T	LOC_Os03g62314.1	upstream_gene_variant ; 672.0bp to feature; MODIFIER	silent_mutation	Average:59.753; most accessible tissue: Minghui63 root, score: 78.091	N	N	N	N
vg0335310058	A -> T	LOC_Os03g62340.1	downstream_gene_variant ; 2393.0bp to feature; MODIFIER	silent_mutation	Average:59.753; most accessible tissue: Minghui63 root, score: 78.091	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0335310058	NA	2.03E-12	mr1377_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
vg0335310058	NA	4.90E-06	mr1377_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