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Detailed information for vg0321057005:

Variant ID: vg0321057005 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 21057005
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:

GTACAGATTAATGCACACACCCAAATCCATTCTGAAAAGGCCTACTATTCATTGGAAAATGTAACTTTCTAGCAGACGAGGAAAATGTGCAATCTTGTTG[G/A]
ACTTCAAATAAAAGATTTGTATATCCGCCTTGGATCAAAGGAGTAGGCATGGTCGAAGATTCACCATATACATCATTTGCAACCATGGTTGAAGATTGCC

Reverse complement sequence

GGCAATCTTCAACCATGGTTGCAAATGATGTATATGGTGAATCTTCGACCATGCCTACTCCTTTGATCCAAGGCGGATATACAAATCTTTTATTTGAAGT[C/T]
CAACAAGATTGCACATTTTCCTCGTCTGCTAGAAAGTTACATTTTCCAATGAATAGTAGGCCTTTTCAGAATGGATTTGGGTGTGTGCATTAATCTGTAC

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	93.80%	5.00%	1.16%	0.00%	NA
All Indica	2759	99.70%	0.30%	0.07%	0.00%	NA
All Japonica	1512	81.50%	15.00%	3.44%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	98.90%	0.90%	0.22%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.10%	0.13%	0.00%	NA
Temperate Japonica	767	65.80%	28.30%	5.87%	0.00%	NA
Tropical Japonica	504	99.20%	0.20%	0.60%	0.00%	NA
Japonica Intermediate	241	94.60%	3.70%	1.66%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	1.10%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0321057005	G -> A	LOC_Os03g37920.1	3_prime_UTR_variant ; 201.0bp to feature; MODIFIER	silent_mutation	Average:43.95; most accessible tissue: Callus, score: 85.284	N	N	N	N
vg0321057005	G -> A	LOC_Os03g37915.1	upstream_gene_variant ; 1478.0bp to feature; MODIFIER	silent_mutation	Average:43.95; most accessible tissue: Callus, score: 85.284	N	N	N	N
vg0321057005	G -> A	LOC_Os03g37930.1	downstream_gene_variant ; 3408.0bp to feature; MODIFIER	silent_mutation	Average:43.95; most accessible tissue: Callus, score: 85.284	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0321057005	5.14E-06	NA	mr1210	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
vg0321057005	NA	3.72E-07	mr1210	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
vg0321057005	NA	1.46E-06	mr1305	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
vg0321057005	NA	4.40E-07	mr1585	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
vg0321057005	4.21E-06	NA	mr1586	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
vg0321057005	NA	1.22E-06	mr1586	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
vg0321057005	6.05E-07	NA	mr1765	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
vg0321057005	NA	2.29E-08	mr1765	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
vg0321057005	NA	1.23E-06	mr1305_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
vg0321057005	NA	3.33E-07	mr1585_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
vg0321057005	NA	5.50E-07	mr1585_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
vg0321057005	NA	7.15E-06	mr1793_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