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Detailed information for vg0234359485:

Variant ID: vg0234359485 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 34359485
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTGCGAGGCAAATTTTTTAAACCTAATTAATCCATAATTAGAGAATGTTTACTGTAGCATCACATAGGCTAATCATGGATTAATTAGGCTCAATAGATTC[G/A]
TCTCGCGAATTAGTCCAAGATTATGGATTGGTTTTATTAATAGTCTACGTTTAATATTTATAATTAGTGTCCAAACATCCGATGTGATAGCGACTTAAAA

Reverse complement sequence

TTTTAAGTCGCTATCACATCGGATGTTTGGACACTAATTATAAATATTAAACGTAGACTATTAATAAAACCAATCCATAATCTTGGACTAATTCGCGAGA[C/T]
GAATCTATTGAGCCTAATTAATCCATGATTAGCCTATGTGATGCTACAGTAAACATTCTCTAATTATGGATTAATTAGGTTTAAAAAATTTGCCTCGCAA

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	94.10%	3.20%	2.69%	0.00%	NA
All Indica	2759	95.90%	2.40%	1.70%	0.00%	NA
All Japonica	1512	98.70%	0.50%	0.73%	0.00%	NA
Aus	269	67.70%	21.60%	10.78%	0.00%	NA
Indica I	595	99.20%	0.20%	0.67%	0.00%	NA
Indica II	465	95.70%	3.40%	0.86%	0.00%	NA
Indica III	913	93.10%	3.30%	3.61%	0.00%	NA
Indica Intermediate	786	96.80%	2.40%	0.76%	0.00%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	98.00%	0.80%	1.19%	0.00%	NA
Japonica Intermediate	241	96.70%	1.70%	1.66%	0.00%	NA
VI/Aromatic	96	41.70%	17.70%	40.62%	0.00%	NA
Intermediate	90	94.40%	4.40%	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
vg0234359485	G -> A	LOC_Os02g56140.1	upstream_gene_variant ; 2698.0bp to feature; MODIFIER	silent_mutation	Average:27.191; most accessible tissue: Callus, score: 71.334	N	N	N	N
vg0234359485	G -> A	LOC_Os02g56160.1	upstream_gene_variant ; 1719.0bp to feature; MODIFIER	silent_mutation	Average:27.191; most accessible tissue: Callus, score: 71.334	N	N	N	N
vg0234359485	G -> A	LOC_Os02g56170.1	downstream_gene_variant ; 2816.0bp to feature; MODIFIER	silent_mutation	Average:27.191; most accessible tissue: Callus, score: 71.334	N	N	N	N
vg0234359485	G -> A	LOC_Os02g56150.1	intron_variant ; MODIFIER	silent_mutation	Average:27.191; most accessible tissue: Callus, score: 71.334	N	N	N	N
vg0234359485	G -> A	LOC_Os02g56150.2	intron_variant ; MODIFIER	silent_mutation	Average:27.191; most accessible tissue: Callus, score: 71.334	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0234359485	4.02E-06	NA	mr1281_2	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
vg0234359485	NA	5.52E-09	mr1567_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
vg0234359485	NA	1.11E-07	mr1765_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
vg0234359485	7.26E-06	NA	mr1829_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
vg0234359485	4.58E-08	NA	mr1842_2	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