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Detailed information for vg0520600456:

Variant ID: vg0520600456 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 20600456
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AACATTGTGGGCGCTATGTGCGAAATAATGGCCCTATTTGGTAATGTACTCCCTCCTTCCCAAAATAAAAGACTTTGTTCAGATTTGTTGTTCTGTGATG[G/A]
GTCACATCTTATTCTATATTAAGTTATTTTGGGATGGAGGGAGTATGTTATTAAAATATTTTTTATTTTTTGACCTAGCTTCATGGTTAATATGTTGTTT

Reverse complement sequence

AAACAACATATTAACCATGAAGCTAGGTCAAAAAATAAAAAATATTTTAATAACATACTCCCTCCATCCCAAAATAACTTAATATAGAATAAGATGTGAC[C/T]
CATCACAGAACAACAAATCTGAACAAAGTCTTTTATTTTGGGAAGGAGGGAGTACATTACCAAATAGGGCCATTATTTCGCACATAGCGCCCACAATGTT

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	56.20%	43.60%	0.11%	0.08%	NA
All Indica	2759	92.30%	7.50%	0.14%	0.11%	NA
All Japonica	1512	2.20%	97.80%	0.00%	0.00%	NA
Aus	269	11.50%	88.50%	0.00%	0.00%	NA
Indica I	595	93.90%	5.70%	0.34%	0.00%	NA
Indica II	465	89.00%	10.80%	0.00%	0.22%	NA
Indica III	913	93.40%	6.50%	0.00%	0.11%	NA
Indica Intermediate	786	91.60%	8.00%	0.25%	0.13%	NA
Temperate Japonica	767	3.80%	96.20%	0.00%	0.00%	NA
Tropical Japonica	504	0.40%	99.60%	0.00%	0.00%	NA
Japonica Intermediate	241	0.80%	99.20%	0.00%	0.00%	NA
VI/Aromatic	96	2.10%	96.90%	1.04%	0.00%	NA
Intermediate	90	50.00%	48.90%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0520600456	G -> DEL	N	N	silent_mutation	Average:66.979; most accessible tissue: Callus, score: 90.854	N	N	N	N
vg0520600456	G -> A	LOC_Os05g34740.1	upstream_gene_variant ; 4887.0bp to feature; MODIFIER	silent_mutation	Average:66.979; most accessible tissue: Callus, score: 90.854	N	N	N	N
vg0520600456	G -> A	LOC_Os05g34720.1	downstream_gene_variant ; 1629.0bp to feature; MODIFIER	silent_mutation	Average:66.979; most accessible tissue: Callus, score: 90.854	N	N	N	N
vg0520600456	G -> A	LOC_Os05g34730.1	downstream_gene_variant ; 805.0bp to feature; MODIFIER	silent_mutation	Average:66.979; most accessible tissue: Callus, score: 90.854	N	N	N	N
vg0520600456	G -> A	LOC_Os05g34720-LOC_Os05g34730	intergenic_region ; MODIFIER	silent_mutation	Average:66.979; most accessible tissue: Callus, score: 90.854	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0520600456	NA	1.31E-33	mr1026	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
vg0520600456	NA	1.09E-34	mr1161	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
vg0520600456	NA	2.58E-14	mr1261	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
vg0520600456	NA	1.38E-10	mr1316	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
vg0520600456	4.34E-06	4.34E-06	mr1428	Ind_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
vg0520600456	NA	4.23E-25	mr1537	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
vg0520600456	NA	1.86E-20	mr1541	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
vg0520600456	NA	6.91E-13	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
vg0520600456	NA	4.56E-59	mr1109_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
vg0520600456	NA	9.42E-20	mr1255_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
vg0520600456	NA	5.18E-30	mr1270_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
vg0520600456	NA	7.64E-24	mr1316_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
vg0520600456	NA	1.55E-09	mr1649_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
vg0520600456	NA	7.17E-15	mr1720_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
vg0520600456	NA	1.62E-31	mr1913_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
vg0520600456	NA	4.18E-30	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