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Detailed information for vg0504371369:

Variant ID: vg0504371369 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 4371369
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

TCCCGTTGTGTCCGCCACCACGGCGTTAAGTTTAAGGCGTGGGCCTGCCACTTAACGGTTCTTGGTTATATAACGTGTATGGCTTAGGATGGAGAGACAC[G/A]
TATCGTGCTGGTGTAAGGCTAAATCATGAATTTTGGAAAAGATTTGTTGTGAGTAATAAATCGGGTACTTATGTATCGCGTGCCATGCTCTTGCATGATT

Reverse complement sequence

AATCATGCAAGAGCATGGCACGCGATACATAAGTACCCGATTTATTACTCACAACAAATCTTTTCCAAAATTCATGATTTAGCCTTACACCAGCACGATA[C/T]
GTGTCTCTCCATCCTAAGCCATACACGTTATATAACCAAGAACCGTTAAGTGGCAGGCCCACGCCTTAAACTTAACGCCGTGGTGGCGGACACAACGGGA

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	94.90%	4.20%	0.93%	0.00%	NA
All Indica	2759	91.30%	7.10%	1.56%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	96.10%	2.70%	1.18%	0.00%	NA
Indica II	465	90.80%	7.30%	1.94%	0.00%	NA
Indica III	913	90.60%	8.70%	0.77%	0.00%	NA
Indica Intermediate	786	88.90%	8.50%	2.54%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0504371369	G -> A	LOC_Os05g08040-LOC_Os05g08050	intergenic_region ; MODIFIER	silent_mutation	Average:53.888; most accessible tissue: Minghui63 young leaf, score: 81.195	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0504371369	4.89E-06	4.89E-06	mr1275	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
vg0504371369	NA	9.88E-06	mr1330	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
vg0504371369	9.43E-08	3.16E-08	mr1352	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
vg0504371369	7.40E-06	7.40E-06	mr1615	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
vg0504371369	8.67E-06	8.67E-06	mr1905	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