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Detailed information for vg0620778091:

Variant ID: vg0620778091 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 20778091
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.94, G: 0.07, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

TAATAATAGTTGACTAAATCTCGGCAGGACCCACCACATACCATGTCTTGGAAACAACCTTTGGATATAGGAGGAGTTCTGCATAAGGAAGGATAACCAG[A/G]
GTTCTACATAGAAACGACAAGTACTACTCGGATTGTATCTATATTGGTTTCCTTAGTTCTACTTGAACAAGGGGAAACCTATGGGTATAAATACAAGGCC

Reverse complement sequence

GGCCTTGTATTTATACCCATAGGTTTCCCCTTGTTCAAGTAGAACTAAGGAAACCAATATAGATACAATCCGAGTAGTACTTGTCGTTTCTATGTAGAAC[T/C]
CTGGTTATCCTTCCTTATGCAGAACTCCTCCTATATCCAAAGGTTGTTTCCAAGACATGGTATGTGGTGGGTCCTGCCGAGATTTAGTCAACTATTATTA

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	54.30%	45.30%	0.23%	0.19%	NA
All Indica	2759	28.30%	71.00%	0.40%	0.25%	NA
All Japonica	1512	94.20%	5.70%	0.00%	0.07%	NA
Aus	269	98.90%	1.10%	0.00%	0.00%	NA
Indica I	595	4.90%	95.10%	0.00%	0.00%	NA
Indica II	465	36.10%	63.70%	0.22%	0.00%	NA
Indica III	913	40.90%	58.40%	0.33%	0.44%	NA
Indica Intermediate	786	27.00%	71.80%	0.89%	0.38%	NA
Temperate Japonica	767	97.50%	2.30%	0.00%	0.13%	NA
Tropical Japonica	504	95.80%	4.20%	0.00%	0.00%	NA
Japonica Intermediate	241	80.50%	19.50%	0.00%	0.00%	NA
VI/Aromatic	96	41.70%	58.30%	0.00%	0.00%	NA
Intermediate	90	57.80%	41.10%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0620778091	A -> G	LOC_Os06g35600.1	downstream_gene_variant ; 3051.0bp to feature; MODIFIER	silent_mutation	Average:42.067; most accessible tissue: Minghui63 young leaf, score: 68.745	N	N	N	N
vg0620778091	A -> G	LOC_Os06g35610.1	downstream_gene_variant ; 932.0bp to feature; MODIFIER	silent_mutation	Average:42.067; most accessible tissue: Minghui63 young leaf, score: 68.745	N	N	N	N
vg0620778091	A -> G	LOC_Os06g35610-LOC_Os06g35620	intergenic_region ; MODIFIER	silent_mutation	Average:42.067; most accessible tissue: Minghui63 young leaf, score: 68.745	N	N	N	N
vg0620778091	A -> DEL	N	N	silent_mutation	Average:42.067; most accessible tissue: Minghui63 young leaf, score: 68.745	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0620778091	NA	9.01E-08	mr1700_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
vg0620778091	1.77E-06	8.24E-07	mr1865_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