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Detailed information for vg0105186659:

Variant ID: vg0105186659 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 5186659
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGGATCGGACGTCCGATCAGGAGAAAAAAATCGGACGCTCGTCCCAGCCATCGGATCGAGGGATTAAATCTCGACCATTGATAGCGCGTCGTCACTGTTC[G/A]
ATGCAAACTTCTCCCGGGCAGCTGCATGCATGCAACTTTTCCCGCGCACAGAATTGCATATGTGACAGGGATAGTTAATGTTTTGTAAGCAAACTTTAAA

Reverse complement sequence

TTTAAAGTTTGCTTACAAAACATTAACTATCCCTGTCACATATGCAATTCTGTGCGCGGGAAAAGTTGCATGCATGCAGCTGCCCGGGAGAAGTTTGCAT[C/T]
GAACAGTGACGACGCGCTATCAATGGTCGAGATTTAATCCCTCGATCCGATGGCTGGGACGAGCGTCCGATTTTTTTCTCCTGATCGGACGTCCGATCCG

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	85.50%	14.20%	0.21%	0.00%	NA
All Indica	2759	80.40%	19.20%	0.36%	0.00%	NA
All Japonica	1512	99.10%	0.90%	0.00%	0.00%	NA
Aus	269	53.90%	46.10%	0.00%	0.00%	NA
Indica I	595	46.90%	52.80%	0.34%	0.00%	NA
Indica II	465	98.10%	1.50%	0.43%	0.00%	NA
Indica III	913	97.70%	2.20%	0.11%	0.00%	NA
Indica Intermediate	786	75.30%	24.00%	0.64%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	97.80%	2.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	0.00%	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
vg0105186659	G -> A	LOC_Os01g09970.1	upstream_gene_variant ; 4268.0bp to feature; MODIFIER	silent_mutation	Average:20.681; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg0105186659	G -> A	LOC_Os01g09960.1	downstream_gene_variant ; 3045.0bp to feature; MODIFIER	silent_mutation	Average:20.681; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg0105186659	G -> A	LOC_Os01g09960-LOC_Os01g09970	intergenic_region ; MODIFIER	silent_mutation	Average:20.681; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0105186659	NA	6.14E-06	mr1166	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
vg0105186659	1.75E-06	NA	mr1210	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
vg0105186659	NA	8.71E-06	mr1316	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
vg0105186659	NA	4.92E-06	mr1445	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
vg0105186659	NA	7.14E-07	mr1485	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
vg0105186659	NA	1.36E-06	mr1511	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
vg0105186659	NA	7.98E-06	mr1511	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
vg0105186659	NA	4.21E-07	mr1574	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
vg0105186659	3.42E-06	3.42E-06	mr1651	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
vg0105186659	NA	6.03E-07	mr1805_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