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Detailed information for vg0223473843:

Variant ID: vg0223473843 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 23473843
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAAGATTTCCAAGTAGAAATCATGAATGTTGGAGAGCCTCTTATTGTAGTAAAATAACATGGCATCGCATGCCGAGATGTCGAGGCATGATGACAAAGAC[G/A]
TCGTGGTTGGTGAAGTAGTAAAACTTGCGAAGTAGCAGCAATAGAGTTTGCCAGTGCCGAAGATAATAAAGATGAAGTCGCTCCACCATGATGACAAAGT

Reverse complement sequence

ACTTTGTCATCATGGTGGAGCGACTTCATCTTTATTATCTTCGGCACTGGCAAACTCTATTGCTGCTACTTCGCAAGTTTTACTACTTCACCAACCACGA[C/T]
GTCTTTGTCATCATGCCTCGACATCTCGGCATGCGATGCCATGTTATTTTACTACAATAAGAGGCTCTCCAACATTCATGATTTCTACTTGGAAATCTTC

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	72.60%	2.30%	2.33%	22.75%	NA
All Indica	2759	70.00%	3.80%	3.15%	23.09%	NA
All Japonica	1512	76.70%	0.20%	1.32%	21.83%	NA
Aus	269	63.90%	0.00%	0.74%	35.32%	NA
Indica I	595	43.70%	0.00%	5.71%	50.59%	NA
Indica II	465	72.70%	14.80%	3.87%	8.60%	NA
Indica III	913	79.00%	0.50%	1.64%	18.84%	NA
Indica Intermediate	786	77.90%	3.80%	2.54%	15.78%	NA
Temperate Japonica	767	86.00%	0.10%	0.39%	13.43%	NA
Tropical Japonica	504	69.60%	0.20%	1.39%	28.77%	NA
Japonica Intermediate	241	61.40%	0.40%	4.15%	34.02%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	83.30%	1.10%	1.11%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0223473843	G -> A	LOC_Os02g38830.1	downstream_gene_variant ; 282.0bp to feature; MODIFIER	silent_mutation	Average:10.643; most accessible tissue: Minghui63 panicle, score: 16.27	N	N	N	N
vg0223473843	G -> A	LOC_Os02g38820-LOC_Os02g38830	intergenic_region ; MODIFIER	silent_mutation	Average:10.643; most accessible tissue: Minghui63 panicle, score: 16.27	N	N	N	N
vg0223473843	G -> DEL	N	N	silent_mutation	Average:10.643; most accessible tissue: Minghui63 panicle, score: 16.27	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0223473843	1.48E-06	1.48E-06	mr1566	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
vg0223473843	NA	2.30E-06	mr1951_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