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Detailed information for vg0224688934:

Variant ID: vg0224688934 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 24688934
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCGATGATAGACAACGAAAATTTCAGGTGGGTAGAGAAGTACCATGAACGATAATACTACCTCCGTTTTTTAATATATGACGCCGTTGACTTTTTCTCAC[G/A]
TGTTTGATCATTCGTCTTATTCAAAAATTTTATACAAATATATAAGATATAAGTCACACTTAAAGTATTATAAGTGATAAAACAACTCATAACAAAATAA

Reverse complement sequence

TTATTTTGTTATGAGTTGTTTTATCACTTATAATACTTTAAGTGTGACTTATATCTTATATATTTGTATAAAATTTTTGAATAAGACGAATGATCAAACA[C/T]
GTGAGAAAAAGTCAACGGCGTCATATATTAAAAAACGGAGGTAGTATTATCGTTCATGGTACTTCTCTACCCACCTGAAATTTTCGTTGTCTATCATCGA

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	83.90%	15.90%	0.21%	0.00%	NA
All Indica	2759	97.50%	2.40%	0.11%	0.00%	NA
All Japonica	1512	57.10%	42.50%	0.40%	0.00%	NA
Aus	269	97.00%	3.00%	0.00%	0.00%	NA
Indica I	595	99.50%	0.30%	0.17%	0.00%	NA
Indica II	465	99.10%	0.60%	0.22%	0.00%	NA
Indica III	913	96.70%	3.20%	0.11%	0.00%	NA
Indica Intermediate	786	96.10%	3.90%	0.00%	0.00%	NA
Temperate Japonica	767	62.50%	37.20%	0.39%	0.00%	NA
Tropical Japonica	504	54.20%	45.80%	0.00%	0.00%	NA
Japonica Intermediate	241	46.10%	52.70%	1.24%	0.00%	NA
VI/Aromatic	96	81.20%	18.80%	0.00%	0.00%	NA
Intermediate	90	77.80%	21.10%	1.11%	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
vg0224688934	G -> A	LOC_Os02g40720.1	upstream_gene_variant ; 1354.0bp to feature; MODIFIER	silent_mutation	Average:56.201; most accessible tissue: Minghui63 root, score: 86.346	N	N	N	N
vg0224688934	G -> A	LOC_Os02g40730.1	upstream_gene_variant ; 1950.0bp to feature; MODIFIER	silent_mutation	Average:56.201; most accessible tissue: Minghui63 root, score: 86.346	N	N	N	N
vg0224688934	G -> A	LOC_Os02g40710.1	downstream_gene_variant ; 3729.0bp to feature; MODIFIER	silent_mutation	Average:56.201; most accessible tissue: Minghui63 root, score: 86.346	N	N	N	N
vg0224688934	G -> A	LOC_Os02g40720-LOC_Os02g40730	intergenic_region ; MODIFIER	silent_mutation	Average:56.201; most accessible tissue: Minghui63 root, score: 86.346	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0224688934	2.13E-06	NA	mr1022	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