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Detailed information for vg0411669926:

Variant ID: vg0411669926 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 11669926
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.07, others allele: 0.00, population size: 70. )

Flanking Sequence (100 bp) in Reference Genome:

ATCATTATTGCTTTCCTTCCGAGAGTCCCCTTTCCCCGTAGTCTCCCTTTATGGCGTGATTCAGGTATCCCGATTGGGCGATGCTTGCCTCTGGACGAGC[G/A]
CGGTTACGAACATACTTCTTCAGAACGCCCATGTACTTCTTGAAAGGAAACATGTTGTGTAGGTACACAGGACCGAGAATACCGATCTCTTTGACAAGGT

Reverse complement sequence

ACCTTGTCAAAGAGATCGGTATTCTCGGTCCTGTGTACCTACACAACATGTTTCCTTTCAAGAAGTACATGGGCGTTCTGAAGAAGTATGTTCGTAACCG[C/T]
GCTCGTCCAGAGGCAAGCATCGCCCAATCGGGATACCTGAATCACGCCATAAAGGGAGACTACGGGGAAAGGGGACTCTCGGAAGGAAAGCAATAATGAT

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	30.20%	5.70%	6.47%	57.62%	NA
All Indica	2759	2.20%	0.20%	7.58%	90.00%	NA
All Japonica	1512	87.40%	11.60%	0.13%	0.86%	NA
Aus	269	1.10%	0.00%	31.97%	66.91%	NA
Indica I	595	1.30%	0.20%	1.01%	97.48%	NA
Indica II	465	4.90%	0.20%	13.33%	81.51%	NA
Indica III	913	1.30%	0.00%	10.19%	88.50%	NA
Indica Intermediate	786	2.40%	0.40%	6.11%	91.09%	NA
Temperate Japonica	767	92.00%	7.60%	0.00%	0.39%	NA
Tropical Japonica	504	89.90%	8.70%	0.20%	1.19%	NA
Japonica Intermediate	241	67.20%	30.70%	0.41%	1.66%	NA
VI/Aromatic	96	6.20%	79.20%	5.21%	9.38%	NA
Intermediate	90	38.90%	14.40%	4.44%	42.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0411669926	G -> DEL	N	N	silent_mutation	Average:12.197; most accessible tissue: Callus, score: 25.707	N	N	N	N
vg0411669926	G -> A	LOC_Os04g20800.1	upstream_gene_variant ; 3470.0bp to feature; MODIFIER	silent_mutation	Average:12.197; most accessible tissue: Callus, score: 25.707	N	N	N	N
vg0411669926	G -> A	LOC_Os04g20790.1	intron_variant ; MODIFIER	silent_mutation	Average:12.197; most accessible tissue: Callus, score: 25.707	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0411669926	7.83E-07	1.15E-08	mr1343	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
vg0411669926	5.17E-07	9.70E-13	mr1829	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
vg0411669926	7.80E-08	8.02E-17	mr1842	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
vg0411669926	NA	1.80E-06	mr1549_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
vg0411669926	NA	1.03E-06	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
vg0411669926	NA	4.58E-14	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
vg0411669926	9.69E-06	3.76E-17	mr1842_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