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Detailed information for vg0808428148:

Variant ID: vg0808428148 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 8428148
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTAAAATTTAGGTCCGTGTTTAGATTCAAACTTTTTTCTTCAAACTTTCAATTTTTTCCGTCACATTAAATGTTTGGATACATGTATGGAGCATTAAAT[G/A]
TGGACGAAAAAAACCAATTACACAGTTTGCATGTAAATCGTGAGACGAATCTTTCGAGCCTAATTACGTCATGATTTGACAATGTGATGCTACAGTAAAC

Reverse complement sequence

GTTTACTGTAGCATCACATTGTCAAATCATGACGTAATTAGGCTCGAAAGATTCGTCTCACGATTTACATGCAAACTGTGTAATTGGTTTTTTTCGTCCA[C/T]
ATTTAATGCTCCATACATGTATCCAAACATTTAATGTGACGGAAAAAATTGAAAGTTTGAAGAAAAAAGTTTGAATCTAAACACGGACCTAAATTTTAAA

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	66.00%	9.60%	7.93%	16.53%	NA
All Indica	2759	51.80%	11.40%	12.21%	24.61%	NA
All Japonica	1512	89.60%	8.40%	1.79%	0.20%	NA
Aus	269	66.20%	0.00%	2.60%	31.23%	NA
Indica I	595	66.70%	7.10%	6.55%	19.66%	NA
Indica II	465	74.60%	4.90%	7.31%	13.12%	NA
Indica III	913	23.80%	21.50%	18.29%	36.47%	NA
Indica Intermediate	786	59.40%	6.90%	12.34%	21.37%	NA
Temperate Japonica	767	98.70%	0.90%	0.13%	0.26%	NA
Tropical Japonica	504	79.60%	16.90%	3.37%	0.20%	NA
Japonica Intermediate	241	81.70%	14.50%	3.73%	0.00%	NA
VI/Aromatic	96	93.80%	0.00%	1.04%	5.21%	NA
Intermediate	90	74.40%	11.10%	3.33%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0808428148	G -> A	LOC_Os08g14090.1	upstream_gene_variant ; 2954.0bp to feature; MODIFIER	silent_mutation	Average:44.719; most accessible tissue: Zhenshan97 flower, score: 83.915	N	N	N	N
vg0808428148	G -> A	LOC_Os08g14070.1	downstream_gene_variant ; 2857.0bp to feature; MODIFIER	silent_mutation	Average:44.719; most accessible tissue: Zhenshan97 flower, score: 83.915	N	N	N	N
vg0808428148	G -> A	LOC_Os08g14070-LOC_Os08g14090	intergenic_region ; MODIFIER	silent_mutation	Average:44.719; most accessible tissue: Zhenshan97 flower, score: 83.915	N	N	N	N
vg0808428148	G -> DEL	N	N	silent_mutation	Average:44.719; most accessible tissue: Zhenshan97 flower, score: 83.915	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0808428148	4.14E-06	NA	mr1050_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
vg0808428148	1.54E-06	1.54E-06	mr1192_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
vg0808428148	6.51E-06	2.23E-06	mr1267_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
vg0808428148	7.19E-07	2.54E-07	mr1312_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
vg0808428148	1.31E-06	1.31E-06	mr1312_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
vg0808428148	6.84E-06	3.62E-06	mr1373_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
vg0808428148	1.41E-06	1.41E-06	mr1373_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
vg0808428148	8.54E-07	6.37E-08	mr1397_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
vg0808428148	NA	4.03E-06	mr1397_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
vg0808428148	1.17E-06	1.17E-06	mr1634_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
vg0808428148	2.68E-06	2.68E-06	mr1634_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
vg0808428148	NA	4.63E-06	mr1652_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
vg0808428148	1.60E-07	1.29E-07	mr1663_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
vg0808428148	1.91E-06	1.91E-06	mr1663_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
vg0808428148	NA	4.89E-06	mr1666_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
vg0808428148	1.54E-07	1.54E-07	mr1674_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
vg0808428148	2.94E-07	2.94E-07	mr1688_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
vg0808428148	7.99E-06	7.99E-06	mr1697_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
vg0808428148	NA	6.68E-06	mr1738_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
vg0808428148	4.34E-07	4.35E-07	mr1822_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
vg0808428148	5.60E-06	1.92E-06	mr1843_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
vg0808428148	2.63E-06	2.63E-06	mr1847_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
vg0808428148	5.47E-06	NA	mr1888_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
vg0808428148	9.71E-06	NA	mr1980_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
vg0808428148	9.67E-07	8.00E-07	mr1982_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