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Detailed information for vg0726854885:

Variant ID: vg0726854885 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 26854885
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: 103. )

Flanking Sequence (100 bp) in Reference Genome:

AGTTCAATGCCATACGTACTGGTAGCATTAAGAAGAACCATTGTAAATCTAACCAAAGATATTACTACCTCCGTCCCAAAATAAGTGCAGCTGTAAATAT[T/C]
CGTGCTCAACGTTTGACCGTCCGTCTTATTTAAAAAATTTGTGAAAAATTTGAAAACATTTAGTCACACATAAAGTACTATTCATGTTTTATCATCTAAT

Reverse complement sequence

ATTAGATGATAAAACATGAATAGTACTTTATGTGTGACTAAATGTTTTCAAATTTTTCACAAATTTTTTAAATAAGACGGACGGTCAAACGTTGAGCACG[A/G]
ATATTTACAGCTGCACTTATTTTGGGACGGAGGTAGTAATATCTTTGGTTAGATTTACAATGGTTCTTCTTAATGCTACCAGTACGTATGGCATTGAACT

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	83.20%	16.70%	0.13%	0.00%	NA
All Indica	2759	98.80%	1.10%	0.11%	0.00%	NA
All Japonica	1512	50.80%	49.00%	0.20%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	99.50%	0.50%	0.00%	0.00%	NA
Indica II	465	97.40%	2.60%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	97.70%	1.90%	0.38%	0.00%	NA
Temperate Japonica	767	35.50%	64.40%	0.13%	0.00%	NA
Tropical Japonica	504	87.90%	11.70%	0.40%	0.00%	NA
Japonica Intermediate	241	22.00%	78.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	81.10%	18.90%	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
vg0726854885	T -> C	LOC_Os07g45000.1	downstream_gene_variant ; 4555.0bp to feature; MODIFIER	silent_mutation	Average:57.238; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N
vg0726854885	T -> C	LOC_Os07g45010.1	downstream_gene_variant ; 263.0bp to feature; MODIFIER	silent_mutation	Average:57.238; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N
vg0726854885	T -> C	LOC_Os07g45010-LOC_Os07g45020	intergenic_region ; MODIFIER	silent_mutation	Average:57.238; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0726854885	NA	9.31E-06	mr1070	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
vg0726854885	NA	2.91E-07	mr1092	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
vg0726854885	NA	6.29E-08	mr1097	Jap_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
vg0726854885	NA	8.21E-06	mr1154	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
vg0726854885	NA	3.62E-06	mr1740	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
vg0726854885	NA	1.29E-06	mr1097_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
vg0726854885	NA	4.03E-08	mr1709_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