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Detailed information for vg1105342594:

Variant ID: vg1105342594 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 5342594
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

GGACTATTCAAGAGTAAATTTGTTCGGTCCCTCAGCCTCTGGTGATTACAAATTTCTAGGTGAGCTCATGAATATGTTGATCAGTGCAGAAGACTACACG[G/A]
TCAACTGAGCAAAGACTACTAGAAATGCATAATAAAACGTCAAACCGCTTCTGGGTAGATGACCTAAGTAACCTAGGGACTGGTTTAGTTCCCAACTTTT

Reverse complement sequence

AAAAGTTGGGAACTAAACCAGTCCCTAGGTTACTTAGGTCATCTACCCAGAAGCGGTTTGACGTTTTATTATGCATTTCTAGTAGTCTTTGCTCAGTTGA[C/T]
CGTGTAGTCTTCTGCACTGATCAACATATTCATGAGCTCACCTAGAAATTTGTAATCACCAGAGGCTGAGGGACCGAACAAATTTACTCTTGAATAGTCC

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	90.10%	9.90%	0.00%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	76.60%	23.40%	0.00%	0.00%	NA
Aus	269	91.10%	8.90%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.60%	0.40%	0.00%	0.00%	NA
Temperate Japonica	767	80.80%	19.20%	0.00%	0.00%	NA
Tropical Japonica	504	82.50%	17.50%	0.00%	0.00%	NA
Japonica Intermediate	241	50.60%	49.40%	0.00%	0.00%	NA
VI/Aromatic	96	22.90%	77.10%	0.00%	0.00%	NA
Intermediate	90	87.80%	12.20%	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
vg1105342594	G -> A	LOC_Os11g09970.1	3_prime_UTR_variant ; 332.0bp to feature; MODIFIER	silent_mutation	Average:67.45; most accessible tissue: Zhenshan97 root, score: 77.733	N	N	N	N
vg1105342594	G -> A	LOC_Os11g09960.1	upstream_gene_variant ; 2089.0bp to feature; MODIFIER	silent_mutation	Average:67.45; most accessible tissue: Zhenshan97 root, score: 77.733	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1105342594	NA	3.97E-07	mr1057_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