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Detailed information for vg1123640085:

Variant ID: vg1123640085 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 23640085
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACCTCCTTACCTAATATAAGGATGTTCACTATTTTATTATAACGTTTGACCACTCGTCTTATTCAAAAAATTTGTGCAAATATAAAAAATAAAAAGTTGT[G/A]
GTTAAAGTACTTTGGATAATAATAAAGTAAGTCACAAATATAATAAATAATAATTATAAAATAGTTTTAATAAGATAAATGGCTAAACAGTGCTAGTAAA

Reverse complement sequence

TTTACTAGCACTGTTTAGCCATTTATCTTATTAAAACTATTTTATAATTATTATTTATTATATTTGTGACTTACTTTATTATTATCCAAAGTACTTTAAC[C/T]
ACAACTTTTTATTTTTTATATTTGCACAAATTTTTTGAATAAGACGAGTGGTCAAACGTTATAATAAAATAGTGAACATCCTTATATTAGGTAAGGAGGT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	76.10%	15.40%	0.17%	8.38%	NA
All Indica	2759	62.80%	24.60%	0.22%	12.32%	NA
All Japonica	1512	96.60%	1.90%	0.00%	1.59%	NA
Aus	269	96.70%	0.70%	0.00%	2.60%	NA
Indica I	595	66.90%	25.20%	0.17%	7.73%	NA
Indica II	465	31.00%	42.40%	0.22%	26.45%	NA
Indica III	913	77.20%	11.50%	0.22%	11.06%	NA
Indica Intermediate	786	61.80%	29.00%	0.25%	8.91%	NA
Temperate Japonica	767	96.90%	0.80%	0.00%	2.35%	NA
Tropical Japonica	504	97.40%	2.00%	0.00%	0.60%	NA
Japonica Intermediate	241	93.80%	5.00%	0.00%	1.24%	NA
VI/Aromatic	96	81.20%	3.10%	1.04%	14.58%	NA
Intermediate	90	72.20%	14.40%	1.11%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1123640085	G -> A	LOC_Os11g39680.1	downstream_gene_variant ; 3952.0bp to feature; MODIFIER	silent_mutation	Average:29.01; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg1123640085	G -> A	LOC_Os11g39690.1	downstream_gene_variant ; 168.0bp to feature; MODIFIER	silent_mutation	Average:29.01; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg1123640085	G -> A	LOC_Os11g39680-LOC_Os11g39690	intergenic_region ; MODIFIER	silent_mutation	Average:29.01; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg1123640085	G -> DEL	N	N	silent_mutation	Average:29.01; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1123640085	8.46E-08	5.63E-08	mr1309	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
vg1123640085	NA	1.42E-06	mr1841_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