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Detailed information for vg0138754947:

Variant ID: vg0138754947 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 38754947
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.08, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

ACATTCTGATGAGTATCAGAAACCTCTCTGAATTGAGGTGATAAGTAATAGATGTTTGTCTTAACATGTTCAAATTATACCTGGGAAAAAAGTTCAATTC[G/A]
CTCACTCAATACCAGTGAAAATATTAATTACCATTTACCAGGTCATGATTTCGTTCTAAATCAACAAGACCAGCAGATCAGCAAGTAACCTTGTGCAAAT

Reverse complement sequence

ATTTGCACAAGGTTACTTGCTGATCTGCTGGTCTTGTTGATTTAGAACGAAATCATGACCTGGTAAATGGTAATTAATATTTTCACTGGTATTGAGTGAG[C/T]
GAATTGAACTTTTTTCCCAGGTATAATTTGAACATGTTAAGACAAACATCTATTACTTATCACCTCAATTCAGAGAGGTTTCTGATACTCATCAGAATGT

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	60.40%	35.10%	0.32%	4.15%	NA
All Indica	2759	96.60%	1.20%	0.04%	2.17%	NA
All Japonica	1512	6.90%	93.10%	0.00%	0.00%	NA
Aus	269	12.60%	32.30%	5.20%	49.81%	NA
Indica I	595	94.50%	0.30%	0.17%	5.04%	NA
Indica II	465	98.90%	0.90%	0.00%	0.22%	NA
Indica III	913	96.30%	2.00%	0.00%	1.75%	NA
Indica Intermediate	786	97.10%	1.30%	0.00%	1.65%	NA
Temperate Japonica	767	2.90%	97.10%	0.00%	0.00%	NA
Tropical Japonica	504	13.90%	86.10%	0.00%	0.00%	NA
Japonica Intermediate	241	5.40%	94.60%	0.00%	0.00%	NA
VI/Aromatic	96	4.20%	95.80%	0.00%	0.00%	NA
Intermediate	90	54.40%	43.30%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0138754947	G -> A	LOC_Os01g66720.1	3_prime_UTR_variant ; 92.0bp to feature; MODIFIER	silent_mutation	Average:66.545; most accessible tissue: Callus, score: 80.69	N	N	N	N
vg0138754947	G -> A	LOC_Os01g66740.1	upstream_gene_variant ; 4810.0bp to feature; MODIFIER	silent_mutation	Average:66.545; most accessible tissue: Callus, score: 80.69	N	N	N	N
vg0138754947	G -> A	LOC_Os01g66710.1	downstream_gene_variant ; 4179.0bp to feature; MODIFIER	silent_mutation	Average:66.545; most accessible tissue: Callus, score: 80.69	N	N	N	N
vg0138754947	G -> A	LOC_Os01g66730.1	downstream_gene_variant ; 111.0bp to feature; MODIFIER	silent_mutation	Average:66.545; most accessible tissue: Callus, score: 80.69	N	N	N	N
vg0138754947	G -> A	LOC_Os01g66730.2	downstream_gene_variant ; 139.0bp to feature; MODIFIER	silent_mutation	Average:66.545; most accessible tissue: Callus, score: 80.69	N	N	N	N
vg0138754947	G -> DEL	N	N	silent_mutation	Average:66.545; most accessible tissue: Callus, score: 80.69	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0138754947	NA	5.47E-24	mr1841	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
vg0138754947	NA	3.17E-06	mr1672_2	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
vg0138754947	NA	9.26E-07	mr1946_2	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
vg0138754947	NA	9.26E-07	mr1948_2	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