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Detailed information for vg0320137682:

Variant ID: vg0320137682 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 20137682
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CACCTCACTTTGTGTTTTCTAAAATCGTTGCTTATATATCCTTTGTTCCTTGTTTCTCAATGATGGCTACCCGCATTCACCGTGGTTGTCGAGAGCCCAC[G/A]
CCGGAGCCCGTGAGTGAGCATGAGGAATCGAGCAGACAGGAATATGCTCAAAGCGAGGAAGAATTTGTAGAAGAAGTTGAGGGGGTTGAGGAGGAAGCTA

Reverse complement sequence

TAGCTTCCTCCTCAACCCCCTCAACTTCTTCTACAAATTCTTCCTCGCTTTGAGCATATTCCTGTCTGCTCGATTCCTCATGCTCACTCACGGGCTCCGG[C/T]
GTGGGCTCTCGACAACCACGGTGAATGCGGGTAGCCATCATTGAGAAACAAGGAACAAAGGATATATAAGCAACGATTTTAGAAAACACAAAGTGAGGTG

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	61.20%	32.90%	0.32%	5.63%	NA
All Indica	2759	87.10%	3.40%	0.40%	9.13%	NA
All Japonica	1512	12.00%	87.20%	0.00%	0.79%	NA
Aus	269	89.60%	10.00%	0.37%	0.00%	NA
Indica I	595	62.40%	6.20%	1.18%	30.25%	NA
Indica II	465	94.40%	3.00%	0.00%	2.58%	NA
Indica III	913	98.70%	1.10%	0.11%	0.11%	NA
Indica Intermediate	786	88.00%	4.10%	0.38%	7.51%	NA
Temperate Japonica	767	0.30%	99.70%	0.00%	0.00%	NA
Tropical Japonica	504	31.90%	65.70%	0.00%	2.38%	NA
Japonica Intermediate	241	7.50%	92.50%	0.00%	0.00%	NA
VI/Aromatic	96	25.00%	75.00%	0.00%	0.00%	NA
Intermediate	90	45.60%	48.90%	3.33%	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
vg0320137682	G -> A	LOC_Os03g36290.1	upstream_gene_variant ; 4140.0bp to feature; MODIFIER	silent_mutation	Average:43.426; most accessible tissue: Zhenshan97 young leaf, score: 78.644	N	N	N	N
vg0320137682	G -> A	LOC_Os03g36300.1	upstream_gene_variant ; 149.0bp to feature; MODIFIER	silent_mutation	Average:43.426; most accessible tissue: Zhenshan97 young leaf, score: 78.644	N	N	N	N
vg0320137682	G -> A	LOC_Os03g36310.1	upstream_gene_variant ; 374.0bp to feature; MODIFIER	silent_mutation	Average:43.426; most accessible tissue: Zhenshan97 young leaf, score: 78.644	N	N	N	N
vg0320137682	G -> A	LOC_Os03g36300-LOC_Os03g36310	intergenic_region ; MODIFIER	silent_mutation	Average:43.426; most accessible tissue: Zhenshan97 young leaf, score: 78.644	N	N	N	N
vg0320137682	G -> DEL	N	N	silent_mutation	Average:43.426; most accessible tissue: Zhenshan97 young leaf, score: 78.644	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0320137682	NA	3.38E-07	mr1136	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
vg0320137682	NA	5.35E-12	mr1188	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
vg0320137682	NA	1.48E-07	mr1217	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
vg0320137682	NA	2.41E-06	mr1830	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
vg0320137682	NA	4.09E-07	mr1845	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
vg0320137682	NA	7.10E-08	mr1852	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
vg0320137682	NA	1.76E-08	mr1136_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
vg0320137682	NA	1.89E-14	mr1188_2	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
vg0320137682	NA	2.08E-06	mr1188_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
vg0320137682	5.33E-08	5.01E-12	mr1750_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