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Detailed information for vg0518836423:

Variant ID: vg0518836423 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 18836423
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: 268. )

Flanking Sequence (100 bp) in Reference Genome:

GGCACGTCCGCATCTCACCAACCTTTGGACCTGCACTGGAGCTAAGCAGATATCCCAGGCCGTTGTGTTCATCAACTTAGTTTGCGCCAACACAGATCCG[G/A]
CACCACTGGCCGAGTGCGGATTTTTCGTCGATAGCCGTGGAGTGAAGCTTCACTTTCTTTTATTGGCCGCCACCATATAAAGTAATAATTCGTGGAGTGA

Reverse complement sequence

TCACTCCACGAATTATTACTTTATATGGTGGCGGCCAATAAAAGAAAGTGAAGCTTCACTCCACGGCTATCGACGAAAAATCCGCACTCGGCCAGTGGTG[C/T]
CGGATCTGTGTTGGCGCAAACTAAGTTGATGAACACAACGGCCTGGGATATCTGCTTAGCTCCAGTGCAGGTCCAAAGGTTGGTGAGATGCGGACGTGCC

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	95.20%	4.80%	0.04%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	91.30%	8.60%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	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	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.30%	0.00%	0.00%	NA
Temperate Japonica	767	98.20%	1.80%	0.00%	0.00%	NA
Tropical Japonica	504	79.00%	20.80%	0.20%	0.00%	NA
Japonica Intermediate	241	95.40%	4.60%	0.00%	0.00%	NA
VI/Aromatic	96	9.40%	90.60%	0.00%	0.00%	NA
Intermediate	90	92.20%	6.70%	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
vg0518836423	G -> A	LOC_Os05g32310.1	downstream_gene_variant ; 1910.0bp to feature; MODIFIER	silent_mutation	Average:54.855; most accessible tissue: Zhenshan97 panicle, score: 73.605	N	N	N	N
vg0518836423	G -> A	LOC_Os05g32300-LOC_Os05g32310	intergenic_region ; MODIFIER	silent_mutation	Average:54.855; most accessible tissue: Zhenshan97 panicle, score: 73.605	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0518836423	4.02E-06	2.27E-07	mr1913	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