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Detailed information for vg0529056354:

Variant ID: vg0529056354 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 29056354
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.03, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

CCACAGCCATTTGTGCCACTGGATGAGCACTGCCATGACCGTGCCTTACCGCGATTCCGTCTCGTCCTTCTCCATTCCCAGCAATGCAACCACAACCGTC[A/G]
CCGCCGTTGTGCGGCCGACCTCGCGTGGTTTCGCTACCTCAACCCTCAGGGCACCGCCCACCACCGCACCACCATTCCCGACCACTCCGACCGCCAAGGT

Reverse complement sequence

ACCTTGGCGGTCGGAGTGGTCGGGAATGGTGGTGCGGTGGTGGGCGGTGCCCTGAGGGTTGAGGTAGCGAAACCACGCGAGGTCGGCCGCACAACGGCGG[T/C]
GACGGTTGTGGTTGCATTGCTGGGAATGGAGAAGGACGAGACGGAATCGCGGTAAGGCACGGTCATGGCAGTGCTCATCCAGTGGCACAAATGGCTGTGG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	62.10%	37.80%	0.13%	0.00%	NA
All Indica	2759	49.40%	50.40%	0.18%	0.00%	NA
All Japonica	1512	93.70%	6.20%	0.07%	0.00%	NA
Aus	269	0.00%	100.00%	0.00%	0.00%	NA
Indica I	595	76.50%	23.50%	0.00%	0.00%	NA
Indica II	465	45.40%	54.20%	0.43%	0.00%	NA
Indica III	913	39.90%	60.00%	0.11%	0.00%	NA
Indica Intermediate	786	42.40%	57.40%	0.25%	0.00%	NA
Temperate Japonica	767	90.70%	9.10%	0.13%	0.00%	NA
Tropical Japonica	504	98.80%	1.20%	0.00%	0.00%	NA
Japonica Intermediate	241	92.50%	7.50%	0.00%	0.00%	NA
VI/Aromatic	96	90.60%	9.40%	0.00%	0.00%	NA
Intermediate	90	74.40%	25.60%	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
vg0529056354	A -> G	LOC_Os05g50680.1	downstream_gene_variant ; 3917.0bp to feature; MODIFIER	silent_mutation	Average:52.036; most accessible tissue: Zhenshan97 young leaf, score: 74.302	N	N	N	N
vg0529056354	A -> G	LOC_Os05g50690.1	downstream_gene_variant ; 1889.0bp to feature; MODIFIER	silent_mutation	Average:52.036; most accessible tissue: Zhenshan97 young leaf, score: 74.302	N	N	N	N
vg0529056354	A -> G	LOC_Os05g50680-LOC_Os05g50690	intergenic_region ; MODIFIER	silent_mutation	Average:52.036; most accessible tissue: Zhenshan97 young leaf, score: 74.302	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0529056354	2.01E-06	2.01E-06	mr1430_2	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
vg0529056354	NA	4.27E-07	mr1807_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