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Detailed information for vg0620026942:

Variant ID: vg0620026942 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 20026942
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 322. )

Flanking Sequence (100 bp) in Reference Genome:

AGGCAATTTATGTTCATGTCAAGGTATTTTTAAGAATGCACAGAAAGCTGCTTTTCACATTGCTGTTGCCAATTATTAGCAAATTCTTAAACTTTAAAAG[G/T]
CAGCATTTTGTAGTGTATCTAAATTTTGGTTCAGATTATGTATTGTTAGTGGCTCATCTTTGTATTTCAGTATAATTAATCATGCGTCTCATTGATTCAA

Reverse complement sequence

TTGAATCAATGAGACGCATGATTAATTATACTGAAATACAAAGATGAGCCACTAACAATACATAATCTGAACCAAAATTTAGATACACTACAAAATGCTG[C/A]
CTTTTAAAGTTTAAGAATTTGCTAATAATTGGCAACAGCAATGTGAAAAGCAGCTTTCTGTGCATTCTTAAAAATACCTTGACATGAACATAAATTGCCT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	96.80%	2.60%	0.57%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	90.10%	8.10%	1.72%	0.00%	NA
Aus	269	100.00%	0.00%	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	84.60%	12.10%	3.26%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	87.10%	12.40%	0.41%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	0.00%	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
vg0620026942	G -> T	LOC_Os06g34410.1	upstream_gene_variant ; 1615.0bp to feature; MODIFIER	silent_mutation	Average:42.074; most accessible tissue: Callus, score: 82.324	N	N	N	N
vg0620026942	G -> T	LOC_Os06g34420.1	intron_variant ; MODIFIER	silent_mutation	Average:42.074; most accessible tissue: Callus, score: 82.324	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0620026942	4.97E-06	7.02E-07	mr1037_2	Jap_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