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Detailed information for vg0903033282:

Variant ID: vg0903033282 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 3033282
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: 254. )

Flanking Sequence (100 bp) in Reference Genome:

ACTGCCGAGTTCCTTGCGACAGCCCGTCATAACCATACAACCGGGGCTAAATACGGAGGAATACCCTCCCCGAGGAATTAACTTAGGATTATATACCGGC[G/A]
CGGAGGAATACCCGTACTGAGCTGTCACCATCAGCGGCCCACCTCTCATCTGCAATATATAACCCCAAATAATGATATCCCGTAATCTAGACCACGTCTA

Reverse complement sequence

TAGACGTGGTCTAGATTACGGGATATCATTATTTGGGGTTATATATTGCAGATGAGAGGTGGGCCGCTGATGGTGACAGCTCAGTACGGGTATTCCTCCG[C/T]
GCCGGTATATAATCCTAAGTTAATTCCTCGGGGAGGGTATTCCTCCGTATTTAGCCCCGGTTGTATGGTTATGACGGGCTGTCGCAAGGAACTCGGCAGT

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	97.10%	1.70%	1.27%	0.00%	NA
All Indica	2759	99.70%	0.10%	0.18%	0.00%	NA
All Japonica	1512	91.70%	5.10%	3.24%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.50%	0.20%	0.34%	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	99.60%	0.00%	0.38%	0.00%	NA
Temperate Japonica	767	84.70%	9.60%	5.61%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	96.70%	1.20%	2.07%	0.00%	NA
VI/Aromatic	96	95.80%	0.00%	4.17%	0.00%	NA
Intermediate	90	97.80%	0.00%	2.22%	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
vg0903033282	G -> A	LOC_Os09g06430.1	upstream_gene_variant ; 2923.0bp to feature; MODIFIER	silent_mutation	Average:49.092; most accessible tissue: Zhenshan97 root, score: 66.289	N	N	N	N
vg0903033282	G -> A	LOC_Os09g06440.1	upstream_gene_variant ; 996.0bp to feature; MODIFIER	silent_mutation	Average:49.092; most accessible tissue: Zhenshan97 root, score: 66.289	N	N	N	N
vg0903033282	G -> A	LOC_Os09g06450.1	downstream_gene_variant ; 1717.0bp to feature; MODIFIER	silent_mutation	Average:49.092; most accessible tissue: Zhenshan97 root, score: 66.289	N	N	N	N
vg0903033282	G -> A	LOC_Os09g06440-LOC_Os09g06450	intergenic_region ; MODIFIER	silent_mutation	Average:49.092; most accessible tissue: Zhenshan97 root, score: 66.289	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0903033282	1.32E-07	NA	mr1334	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