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Detailed information for vg0506871977:

Variant ID: vg0506871977 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 6871977
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, G: 0.02, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:

AATTAATAGCTAGATATTTTGCTTTATTTTTTCTTAGAATTTCTCTAATTTATTAGAGCGCCACTTGGCAGCCTAGGAGCGTTTGTAGAGATGTCATGTG[A/G]
CGGCTTAGGAGCATTTGTAGAAAGTTTTATAAACTTTTAGTATTATTTTTTTCTTAGAATTTTTCTAATTTATTAGAGCGCCACTTGACAGTCTAGGAGC

Reverse complement sequence

GCTCCTAGACTGTCAAGTGGCGCTCTAATAAATTAGAAAAATTCTAAGAAAAAAATAATACTAAAAGTTTATAAAACTTTCTACAAATGCTCCTAAGCCG[T/C]
CACATGACATCTCTACAAACGCTCCTAGGCTGCCAAGTGGCGCTCTAATAAATTAGAGAAATTCTAAGAAAAAATAAAGCAAAATATCTAGCTATTAATT

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	42.30%	9.20%	6.14%	42.30%	NA
All Indica	2759	11.90%	12.80%	6.74%	68.54%	NA
All Japonica	1512	95.30%	0.50%	2.84%	1.32%	NA
Aus	269	31.60%	23.40%	20.45%	24.54%	NA
Indica I	595	5.00%	7.90%	6.05%	81.01%	NA
Indica II	465	20.40%	7.10%	5.38%	67.10%	NA
Indica III	913	10.70%	17.70%	7.67%	63.86%	NA
Indica Intermediate	786	13.40%	14.20%	7.00%	65.39%	NA
Temperate Japonica	767	98.40%	0.10%	0.26%	1.17%	NA
Tropical Japonica	504	94.40%	0.60%	3.37%	1.59%	NA
Japonica Intermediate	241	87.10%	1.70%	9.96%	1.24%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	57.80%	12.20%	6.67%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0506871977	A -> DEL	N	N	silent_mutation	Average:43.24; most accessible tissue: Callus, score: 60.287	N	N	N	N
vg0506871977	A -> G	LOC_Os05g12020.1	upstream_gene_variant ; 1850.0bp to feature; MODIFIER	silent_mutation	Average:43.24; most accessible tissue: Callus, score: 60.287	N	N	N	N
vg0506871977	A -> G	LOC_Os05g12010.1	downstream_gene_variant ; 3736.0bp to feature; MODIFIER	silent_mutation	Average:43.24; most accessible tissue: Callus, score: 60.287	N	N	N	N
vg0506871977	A -> G	LOC_Os05g12010-LOC_Os05g12020	intergenic_region ; MODIFIER	silent_mutation	Average:43.24; most accessible tissue: Callus, score: 60.287	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0506871977	9.67E-11	2.52E-40	mr1039	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
vg0506871977	3.36E-08	7.45E-10	mr1039	Ind_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
vg0506871977	NA	3.60E-11	mr1514	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
vg0506871977	NA	2.74E-08	mr1593	Ind_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
vg0506871977	1.31E-08	1.67E-41	mr1632	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
vg0506871977	5.10E-07	2.05E-12	mr1632	Ind_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
vg0506871977	2.80E-09	1.31E-48	mr1873	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
vg0506871977	8.35E-06	4.46E-10	mr1873	Ind_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
vg0506871977	5.76E-12	1.38E-42	mr1039_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
vg0506871977	2.21E-08	6.99E-10	mr1039_2	Ind_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
vg0506871977	4.43E-10	4.77E-20	mr1514_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
vg0506871977	5.75E-07	8.01E-08	mr1514_2	Ind_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
vg0506871977	NA	1.65E-08	mr1593_2	Ind_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
vg0506871977	9.26E-15	4.43E-55	mr1632_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
vg0506871977	8.65E-11	4.03E-15	mr1632_2	Ind_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
vg0506871977	1.96E-07	7.72E-07	mr1750_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
vg0506871977	1.18E-08	1.86E-40	mr1873_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
vg0506871977	2.91E-06	4.19E-08	mr1873_2	Ind_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