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Detailed information for vg0522311777:

Variant ID: vg0522311777 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 22311777
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.03, T: 0.02, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:

ACTCCACGCCATTTTTTCACACACCGGATTTTTCGGAATGTTTCCAAAACAAAACAAATCCGAATTTTCCTGCAGCAAAATAAAACTACAAAAGGAGGCT[G/A]
CATCTGCGCAAGGGTGAGGAGCCAATTTTGCGGACCATTCGACGCGTGCGTCGTGCACGCGCGCCGCCTGCCCTGCCCTGCCAGGCCAGGCGAGGCGAGC

Reverse complement sequence

GCTCGCCTCGCCTGGCCTGGCAGGGCAGGGCAGGCGGCGCGCGTGCACGACGCACGCGTCGAATGGTCCGCAAAATTGGCTCCTCACCCTTGCGCAGATG[C/T]
AGCCTCCTTTTGTAGTTTTATTTTGCTGCAGGAAAATTCGGATTTGTTTTGTTTTGGAAACATTCCGAAAAATCCGGTGTGTGAAAAAATGGCGTGGAGT

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	64.10%	35.20%	0.66%	0.00%	NA
All Indica	2759	39.60%	59.40%	1.05%	0.00%	NA
All Japonica	1512	99.70%	0.30%	0.07%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	35.60%	63.40%	1.01%	0.00%	NA
Indica II	465	51.60%	47.70%	0.65%	0.00%	NA
Indica III	913	32.10%	67.40%	0.55%	0.00%	NA
Indica Intermediate	786	44.10%	53.90%	1.91%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	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	76.70%	22.20%	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
vg0522311777	G -> A	LOC_Os05g38050.1	downstream_gene_variant ; 3374.0bp to feature; MODIFIER	silent_mutation	Average:61.904; most accessible tissue: Minghui63 root, score: 79.522	N	N	N	N
vg0522311777	G -> A	LOC_Os05g38060.1	downstream_gene_variant ; 861.0bp to feature; MODIFIER	silent_mutation	Average:61.904; most accessible tissue: Minghui63 root, score: 79.522	N	N	N	N
vg0522311777	G -> A	LOC_Os05g38050-LOC_Os05g38060	intergenic_region ; MODIFIER	silent_mutation	Average:61.904; most accessible tissue: Minghui63 root, score: 79.522	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0522311777	NA	6.62E-07	mr1058	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
vg0522311777	NA	5.37E-06	mr1528	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
vg0522311777	NA	3.55E-06	mr1568	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
vg0522311777	NA	1.42E-08	mr1637	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
vg0522311777	NA	8.67E-06	mr1735	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
vg0522311777	NA	3.12E-07	mr1785	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
vg0522311777	4.24E-06	NA	mr1802	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
vg0522311777	1.50E-06	1.50E-06	mr1802	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