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Detailed information for vg0223668778:

Variant ID: vg0223668778 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 23668778
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, A: 0.00, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

CTAATCACGGTGAATCTGGTCGACCGCCCATAACCGTGGGCACGGCTATTCGAATAGTTTTACTCAGATCAGAGGTGTACAACTGTACCCACAAGACACA[G/A]
CCCCACAACACATTTCCGTGCGCCGACATGCCACCACGACATACTGGAAAGAGGCCGTGACAGGACCCTTCGCATAACCCCCTCTAACTAATCACACCAC

Reverse complement sequence

GTGGTGTGATTAGTTAGAGGGGGTTATGCGAAGGGTCCTGTCACGGCCTCTTTCCAGTATGTCGTGGTGGCATGTCGGCGCACGGAAATGTGTTGTGGGG[C/T]
TGTGTCTTGTGGGTACAGTTGTACACCTCTGATCTGAGTAAAACTATTCGAATAGCCGTGCCCACGGTTATGGGCGGTCGACCAGATTCACCGTGATTAG

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	76.80%	22.40%	0.85%	0.00%	NA
All Indica	2759	63.80%	35.10%	1.09%	0.00%	NA
All Japonica	1512	95.10%	4.40%	0.53%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	44.70%	51.80%	3.53%	0.00%	NA
Indica II	465	60.90%	39.10%	0.00%	0.00%	NA
Indica III	913	77.40%	22.20%	0.33%	0.00%	NA
Indica Intermediate	786	64.10%	35.10%	0.76%	0.00%	NA
Temperate Japonica	767	97.50%	1.60%	0.91%	0.00%	NA
Tropical Japonica	504	90.50%	9.30%	0.20%	0.00%	NA
Japonica Intermediate	241	97.10%	2.90%	0.00%	0.00%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	81.10%	16.70%	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
vg0223668778	G -> A	LOC_Os02g39170.1	upstream_gene_variant ; 4319.0bp to feature; MODIFIER	silent_mutation	Average:64.508; most accessible tissue: Zhenshan97 panicle, score: 78.302	N	N	N	N
vg0223668778	G -> A	LOC_Os02g39180.1	downstream_gene_variant ; 1615.0bp to feature; MODIFIER	silent_mutation	Average:64.508; most accessible tissue: Zhenshan97 panicle, score: 78.302	N	N	N	N
vg0223668778	G -> A	LOC_Os02g39180-LOC_Os02g39190	intergenic_region ; MODIFIER	silent_mutation	Average:64.508; most accessible tissue: Zhenshan97 panicle, score: 78.302	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0223668778	8.48E-06	3.97E-06	mr1060_2	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
vg0223668778	3.38E-06	6.20E-08	mr1060_2	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
vg0223668778	8.38E-06	8.37E-06	mr1444_2	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