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Detailed information for vg0623114792:

Variant ID: vg0623114792 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 23114792
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGTTCCGACCGAAACTATCCGAATCCGAAAAATGGTCCGGACGGACGGAAACTATCCGAACCAGTTTCATCCCTAGTTAAAAGGGCATACTCGCGAGCAT[G/A]
CGAGTGCGGTGTATGCATACATCTTCCAAGGATTTGAAAAAAGAATTCTAATTCAAAGTCATTATGTTCAAGCAGTTAAAAGAATAAACAAAAACATAGA

Reverse complement sequence

TCTATGTTTTTGTTTATTCTTTTAACTGCTTGAACATAATGACTTTGAATTAGAATTCTTTTTTCAAATCCTTGGAAGATGTATGCATACACCGCACTCG[C/T]
ATGCTCGCGAGTATGCCCTTTTAACTAGGGATGAAACTGGTTCGGATAGTTTCCGTCCGTCCGGACCATTTTTCGGATTCGGATAGTTTCGGTCGGAACT

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	86.30%	0.10%	5.92%	7.66%	NA
All Indica	2759	82.40%	0.10%	7.79%	9.71%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	43.90%	1.90%	21.56%	32.71%	NA
Indica I	595	97.30%	0.00%	0.50%	2.18%	NA
Indica II	465	88.00%	0.00%	1.72%	10.32%	NA
Indica III	913	70.60%	0.10%	15.55%	13.69%	NA
Indica Intermediate	786	81.60%	0.10%	7.89%	10.43%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	93.80%	0.00%	5.21%	1.04%	NA
Intermediate	90	92.20%	0.00%	2.22%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0623114792	G -> A	LOC_Os06g38950.1	upstream_gene_variant ; 1694.0bp to feature; MODIFIER	silent_mutation	Average:41.147; most accessible tissue: Zhenshan97 root, score: 83.59	N	N	N	N
vg0623114792	G -> A	LOC_Os06g38960.1	upstream_gene_variant ; 4266.0bp to feature; MODIFIER	silent_mutation	Average:41.147; most accessible tissue: Zhenshan97 root, score: 83.59	N	N	N	N
vg0623114792	G -> A	LOC_Os06g38960.2	upstream_gene_variant ; 4267.0bp to feature; MODIFIER	silent_mutation	Average:41.147; most accessible tissue: Zhenshan97 root, score: 83.59	N	N	N	N
vg0623114792	G -> A	LOC_Os06g38950-LOC_Os06g38960	intergenic_region ; MODIFIER	silent_mutation	Average:41.147; most accessible tissue: Zhenshan97 root, score: 83.59	N	N	N	N
vg0623114792	G -> DEL	N	N	silent_mutation	Average:41.147; most accessible tissue: Zhenshan97 root, score: 83.59	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0623114792	3.44E-06	NA	mr1540_2	Ind_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