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Detailed information for vg0234789969:

Variant ID: vg0234789969 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 34789969
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 327. )

Flanking Sequence (100 bp) in Reference Genome:

ATTTTGGGAGAAACTGTACTAGTTTCCTTCAAAATCATATGAAATTCCTCTATTCCAAAAATGCCAGTTCCATTCTCATTGTGGAACCCATTGTGCATGC[A/G]
TTCTTAATTTGACCATGCAAGTTATCTATCATATGGTTTCTGCGTGTTTGTAATGAAGTGCTTCTGCACTTATGTTATAGATTTTAGATCCGATGACAGG

Reverse complement sequence

CCTGTCATCGGATCTAAAATCTATAACATAAGTGCAGAAGCACTTCATTACAAACACGCAGAAACCATATGATAGATAACTTGCATGGTCAAATTAAGAA[T/C]
GCATGCACAATGGGTTCCACAATGAGAATGGAACTGGCATTTTTGGAATAGAGGAATTTCATATGATTTTGAAGGAAACTAGTACAGTTTCTCCCAAAAT

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	93.00%	7.00%	0.02%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	78.40%	21.60%	0.07%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	69.20%	30.60%	0.13%	0.00%	NA
Tropical Japonica	504	92.70%	7.30%	0.00%	0.00%	NA
Japonica Intermediate	241	77.60%	22.40%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	3.30%	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
vg0234789969	A -> G	LOC_Os02g56750.1	upstream_gene_variant ; 4276.0bp to feature; MODIFIER	silent_mutation	Average:44.11; most accessible tissue: Callus, score: 82.894	N	N	N	N
vg0234789969	A -> G	LOC_Os02g56740.1	intron_variant ; MODIFIER	silent_mutation	Average:44.11; most accessible tissue: Callus, score: 82.894	N	N	N	N
vg0234789969	A -> G	LOC_Os02g56740.2	intron_variant ; MODIFIER	silent_mutation	Average:44.11; most accessible tissue: Callus, score: 82.894	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0234789969	3.92E-07	NA	mr1930	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
vg0234789969	3.95E-06	3.95E-06	mr1930	Jap_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