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Detailed information for vg0124633522:

Variant ID: vg0124633522 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 24633522
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGACAAGTTACCAAAATTTTGGCAACTTTGCCAAAAGATTGCCAAAATTTGGTAAGGTCTTTTTTGGCGTCAAAGTGAACAGGCCCTTAGGAAGATGTAG[G/A]
GCCTGTTCACTTTGATGCCATTTTTAACCTTACCAAATTTTGGTAAAATTGTCAAAAAAAAGTGGCTACATTTAGTTTGCTGCCAAATTTTAGTAACTAT

Reverse complement sequence

ATAGTTACTAAAATTTGGCAGCAAACTAAATGTAGCCACTTTTTTTTGACAATTTTACCAAAATTTGGTAAGGTTAAAAATGGCATCAAAGTGAACAGGC[C/T]
CTACATCTTCCTAAGGGCCTGTTCACTTTGACGCCAAAAAAGACCTTACCAAATTTTGGCAATCTTTTGGCAAAGTTGCCAAAATTTTGGTAACTTGTCA

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	94.40%	5.60%	0.04%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	83.10%	16.80%	0.13%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	82.10%	17.90%	0.00%	0.00%	NA
Tropical Japonica	504	80.60%	19.20%	0.20%	0.00%	NA
Japonica Intermediate	241	91.30%	8.30%	0.41%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	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
vg0124633522	G -> A	LOC_Os01g43160.1	downstream_gene_variant ; 1190.0bp to feature; MODIFIER	silent_mutation	Average:56.089; most accessible tissue: Minghui63 panicle, score: 78.92	N	N	N	N
vg0124633522	G -> A	LOC_Os01g43170.1	downstream_gene_variant ; 222.0bp to feature; MODIFIER	silent_mutation	Average:56.089; most accessible tissue: Minghui63 panicle, score: 78.92	N	N	N	N
vg0124633522	G -> A	LOC_Os01g43170.2	downstream_gene_variant ; 222.0bp to feature; MODIFIER	silent_mutation	Average:56.089; most accessible tissue: Minghui63 panicle, score: 78.92	N	N	N	N
vg0124633522	G -> A	LOC_Os01g43170.3	downstream_gene_variant ; 243.0bp to feature; MODIFIER	silent_mutation	Average:56.089; most accessible tissue: Minghui63 panicle, score: 78.92	N	N	N	N
vg0124633522	G -> A	LOC_Os01g43160-LOC_Os01g43170	intergenic_region ; MODIFIER	silent_mutation	Average:56.089; most accessible tissue: Minghui63 panicle, score: 78.92	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0124633522	2.04E-09	NA	mr1745_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