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Detailed information for vg0124667372:

Variant ID: vg0124667372 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 24667372
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAGGGAGAAGGGCCACCGCCGCCGCTCGCCAGACGCGCCGCCTCCTTCCCAAACCAAGCGCGCCGCTTCTCCTTCCCCACGCTAGCAGCCCGCCCTGGCT[G/A]
GGGACGACGAGCACGTCGGGCGAGCCGATCTCCCTCGCCCTCGCCGCCACGTCCCTCAGGCTCGCCTCCCTTCTCGCCACCAGCCTGCTCGCCGATTCCG

Reverse complement sequence

CGGAATCGGCGAGCAGGCTGGTGGCGAGAAGGGAGGCGAGCCTGAGGGACGTGGCGGCGAGGGCGAGGGAGATCGGCTCGCCCGACGTGCTCGTCGTCCC[C/T]
AGCCAGGGCGGGCTGCTAGCGTGGGGAAGGAGAAGCGGCGCGCTTGGTTTGGGAAGGAGGCGGCGCGTCTGGCGAGCGGCGGCGGTGGCCCTTCTCCCTT

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	88.60%	11.40%	0.00%	0.00%	NA
All Indica	2759	81.50%	18.50%	0.00%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	94.80%	5.20%	0.00%	0.00%	NA
Indica I	595	95.60%	4.40%	0.00%	0.00%	NA
Indica II	465	94.00%	6.00%	0.00%	0.00%	NA
Indica III	913	68.70%	31.30%	0.00%	0.00%	NA
Indica Intermediate	786	78.20%	21.80%	0.00%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	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	91.10%	8.90%	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
vg0124667372	G -> A	LOC_Os01g43200.1	upstream_gene_variant ; 4513.0bp to feature; MODIFIER	silent_mutation	Average:59.712; most accessible tissue: Zhenshan97 young leaf, score: 80.325	N	N	N	N
vg0124667372	G -> A	LOC_Os01g43180-LOC_Os01g43200	intergenic_region ; MODIFIER	silent_mutation	Average:59.712; most accessible tissue: Zhenshan97 young leaf, score: 80.325	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0124667372	NA	3.86E-07	mr1066	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
vg0124667372	2.50E-07	3.53E-07	mr1438	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
vg0124667372	3.34E-07	5.01E-07	mr1438	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