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Detailed information for vg0505162615:

Variant ID: vg0505162615 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 5162615
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGAATTTTGAACAAGTTTTGTTAAATTTGAAAAACTACTTTGGCTAAATTCACAAAAAAAAAACATTCCTGAAAATTTCGGCGAAATAGTTTCATATAGG[G/A]
CGGGCCTAAATTCATGACTTTTTGAAAGTATTATTCCGGAATTTTGAACCTGGTAACAACTTCAGAGTTTGTGATAGTACTCATTTAAAGTTAACTTAGA

Reverse complement sequence

TCTAAGTTAACTTTAAATGAGTACTATCACAAACTCTGAAGTTGTTACCAGGTTCAAAATTCCGGAATAATACTTTCAAAAAGTCATGAATTTAGGCCCG[C/T]
CCTATATGAAACTATTTCGCCGAAATTTTCAGGAATGTTTTTTTTTTGTGAATTTAGCCAAAGTAGTTTTTCAAATTTAACAAAACTTGTTCAAAATTCA

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	87.70%	7.70%	0.30%	4.30%	NA
All Indica	2759	97.00%	2.20%	0.04%	0.69%	NA
All Japonica	1512	86.20%	13.50%	0.26%	0.07%	NA
Aus	269	32.00%	0.00%	3.35%	64.68%	NA
Indica I	595	98.20%	1.80%	0.00%	0.00%	NA
Indica II	465	99.40%	0.00%	0.00%	0.65%	NA
Indica III	913	98.20%	1.80%	0.00%	0.00%	NA
Indica Intermediate	786	93.40%	4.50%	0.13%	2.04%	NA
Temperate Japonica	767	82.80%	16.90%	0.26%	0.00%	NA
Tropical Japonica	504	87.90%	11.90%	0.20%	0.00%	NA
Japonica Intermediate	241	93.40%	5.80%	0.41%	0.41%	NA
VI/Aromatic	96	6.20%	88.50%	0.00%	5.21%	NA
Intermediate	90	82.20%	13.30%	0.00%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0505162615	G -> DEL	N	N	silent_mutation	Average:48.867; most accessible tissue: Minghui63 flower, score: 65.501	N	N	N	N
vg0505162615	G -> A	LOC_Os05g09230.1	upstream_gene_variant ; 1768.0bp to feature; MODIFIER	silent_mutation	Average:48.867; most accessible tissue: Minghui63 flower, score: 65.501	N	N	N	N
vg0505162615	G -> A	LOC_Os05g09240.1	downstream_gene_variant ; 243.0bp to feature; MODIFIER	silent_mutation	Average:48.867; most accessible tissue: Minghui63 flower, score: 65.501	N	N	N	N
vg0505162615	G -> A	LOC_Os05g09240-LOC_Os05g09250	intergenic_region ; MODIFIER	silent_mutation	Average:48.867; most accessible tissue: Minghui63 flower, score: 65.501	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0505162615	NA	9.73E-07	mr1382	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
vg0505162615	NA	2.26E-10	mr1057_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
vg0505162615	NA	2.15E-06	mr1167_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
vg0505162615	NA	2.52E-06	mr1274_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
vg0505162615	NA	6.31E-06	mr1456_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
vg0505162615	7.40E-08	7.40E-08	mr1587_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
vg0505162615	NA	5.66E-06	mr1792_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