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Detailed information for vg0235583404:

Variant ID: vg0235583404 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 35583404
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTGTTAGCCCCATGTGTCACTCTGTAGCAACTCATTCTGTGAGATTTTAGCTTTCTTTTTATGTCTGTAATGGTGGTGCATTGACTCATCGCGCTACCTT[G/A]
TACATTTCTTTTCTTACTCTTAATATACATTGGCCGGCTATTCTCTGGCCCGGCGAAAAAAGAAAACTCAAGTGAGAATCATGGCTTTCTGGAGAAGGCA

Reverse complement sequence

TGCCTTCTCCAGAAAGCCATGATTCTCACTTGAGTTTTCTTTTTTCGCCGGGCCAGAGAATAGCCGGCCAATGTATATTAAGAGTAAGAAAAGAAATGTA[C/T]
AAGGTAGCGCGATGAGTCAATGCACCACCATTACAGACATAAAAAGAAAGCTAAAATCTCACAGAATGAGTTGCTACAGAGTGACACATGGGGCTAACAA

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	60.70%	39.10%	0.15%	0.02%	NA
All Indica	2759	96.40%	3.50%	0.14%	0.00%	NA
All Japonica	1512	4.40%	95.60%	0.00%	0.00%	NA
Aus	269	30.90%	68.00%	0.74%	0.37%	NA
Indica I	595	96.60%	3.40%	0.00%	0.00%	NA
Indica II	465	97.20%	2.20%	0.65%	0.00%	NA
Indica III	913	98.00%	2.00%	0.00%	0.00%	NA
Indica Intermediate	786	93.80%	6.10%	0.13%	0.00%	NA
Temperate Japonica	767	6.10%	93.90%	0.00%	0.00%	NA
Tropical Japonica	504	2.40%	97.60%	0.00%	0.00%	NA
Japonica Intermediate	241	3.30%	96.70%	0.00%	0.00%	NA
VI/Aromatic	96	19.80%	80.20%	0.00%	0.00%	NA
Intermediate	90	44.40%	54.40%	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
vg0235583404	G -> A	LOC_Os02g58160.1	upstream_gene_variant ; 580.0bp to feature; MODIFIER	silent_mutation	Average:66.455; most accessible tissue: Zhenshan97 root, score: 85.677	N	N	N	N
vg0235583404	G -> A	LOC_Os02g58150.1	upstream_gene_variant ; 1557.0bp to feature; MODIFIER	silent_mutation	Average:66.455; most accessible tissue: Zhenshan97 root, score: 85.677	N	N	N	N
vg0235583404	G -> A	LOC_Os02g58160.2	upstream_gene_variant ; 1191.0bp to feature; MODIFIER	silent_mutation	Average:66.455; most accessible tissue: Zhenshan97 root, score: 85.677	N	N	N	N
vg0235583404	G -> A	LOC_Os02g58160-LOC_Os02g58150	intergenic_region ; MODIFIER	silent_mutation	Average:66.455; most accessible tissue: Zhenshan97 root, score: 85.677	N	N	N	N
vg0235583404	G -> DEL	N	N	silent_mutation	Average:66.455; most accessible tissue: Zhenshan97 root, score: 85.677	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0235583404	NA	1.20E-19	mr1021	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
vg0235583404	NA	3.11E-11	mr1657	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
vg0235583404	NA	3.93E-61	mr1064_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
vg0235583404	NA	1.25E-38	mr1745_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
vg0235583404	NA	5.85E-11	mr1781_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
vg0235583404	NA	4.47E-29	mr1932_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
vg0235583404	NA	4.92E-64	mr1970_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
vg0235583404	1.97E-06	1.53E-103	mr1973_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