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Detailed information for vg0234719079:

Variant ID: vg0234719079 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 34719079
Reference Allele: A	Alternative Allele: G
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: 241. )

Flanking Sequence (100 bp) in Reference Genome:

CATGTGGTGTCGGTGTGTTTGAAAATAAAATGAATTGTGAAAATTCGCGATGCGGGTGCCGTGCCTATGTGGCACTGTCTCGTATTTGCATATAAGGACC[A/G]
ATTCCTGTGGGAAACTCATCAAGCATAACAAAGTGCAACCACAAGGTGGAATGGGACACCCTGGCTAAGTAACTAGTCGGTTCAGGGAAACCTCGCATGC

Reverse complement sequence

GCATGCGAGGTTTCCCTGAACCGACTAGTTACTTAGCCAGGGTGTCCCATTCCACCTTGTGGTTGCACTTTGTTATGCTTGATGAGTTTCCCACAGGAAT[T/C]
GGTCCTTATATGCAAATACGAGACAGTGCCACATAGGCACGGCACCCGCATCGCGAATTTTCACAATTCATTTTATTTTCAAACACACCGACACCACATG

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	84.90%	5.40%	3.79%	5.90%	NA
All Indica	2759	98.00%	0.20%	0.72%	1.05%	NA
All Japonica	1512	78.20%	15.80%	5.36%	0.66%	NA
Aus	269	11.90%	1.10%	23.05%	63.94%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	97.80%	0.20%	0.65%	1.29%	NA
Indica III	913	98.60%	0.40%	0.77%	0.22%	NA
Indica Intermediate	786	95.90%	0.10%	1.27%	2.67%	NA
Temperate Japonica	767	62.80%	28.70%	8.34%	0.13%	NA
Tropical Japonica	504	99.00%	0.20%	0.40%	0.40%	NA
Japonica Intermediate	241	83.40%	7.50%	6.22%	2.90%	NA
VI/Aromatic	96	28.10%	0.00%	10.42%	61.46%	NA
Intermediate	90	73.30%	10.00%	6.67%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0234719079	A -> G	LOC_Os02g56630.1	upstream_gene_variant ; 1787.0bp to feature; MODIFIER	silent_mutation	Average:39.126; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg0234719079	A -> G	LOC_Os02g56620-LOC_Os02g56630	intergenic_region ; MODIFIER	silent_mutation	Average:39.126; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg0234719079	A -> DEL	N	N	silent_mutation	Average:39.126; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0234719079	7.18E-06	3.42E-08	mr1872	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