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Detailed information for vg0503179544:

Variant ID: vg0503179544 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 3179544
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:

GGTCCAGGGTTCACTGCTCTAGCGGCTGCATCAACTCCCTCGTCGCCGAGGTAAATTTTATTTATTTATTGAGTTGAATGCGTGCACCAACTAATTCAAC[G/A]
TAAAGCTTAAACCTGACGAGCGATTCACTTATAATGCAATGATATTTAAGGGTAACTAATAAGGGACGGGATCCCATCAAAACATTTAAGGGACAATGAA

Reverse complement sequence

TTCATTGTCCCTTAAATGTTTTGATGGGATCCCGTCCCTTATTAGTTACCCTTAAATATCATTGCATTATAAGTGAATCGCTCGTCAGGTTTAAGCTTTA[C/T]
GTTGAATTAGTTGGTGCACGCATTCAACTCAATAAATAAATAAAATTTACCTCGGCGACGAGGGAGTTGATGCAGCCGCTAGAGCAGTGAACCCTGGACC

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	97.90%	1.10%	0.97%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	93.70%	3.20%	3.04%	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	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	88.10%	6.40%	5.48%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	0.00%	1.66%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	2.20%	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
vg0503179544	G -> A	LOC_Os05g06260.1	downstream_gene_variant ; 2022.0bp to feature; MODIFIER	silent_mutation	Average:71.561; most accessible tissue: Zhenshan97 panicle, score: 85.665	N	N	N	N
vg0503179544	G -> A	LOC_Os05g06250.1	intron_variant ; MODIFIER	silent_mutation	Average:71.561; most accessible tissue: Zhenshan97 panicle, score: 85.665	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0503179544	3.53E-06	4.35E-06	mr1453	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
vg0503179544	5.84E-06	5.84E-06	mr1728	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