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Detailed information for vg0222034653:

Variant ID: vg0222034653 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 22034653
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCAGCTCTTTATTTATACTACACTTCTTTTATGTTATGAGTGTCTTATTTGTTCTTTGTGATGTGATGTTGATTTTATCCTTTTGAGTGCTCACCATGTC[G/A]
TATCTTTTGCATATCATATCTATTCTTACTGCTTATTTGCATCCCAGATGAAGGAAACTCTCTTCGGTTGCTCCCATTAATATATGCATATGAGCTTCAC

Reverse complement sequence

GTGAAGCTCATATGCATATATTAATGGGAGCAACCGAAGAGAGTTTCCTTCATCTGGGATGCAAATAAGCAGTAAGAATAGATATGATATGCAAAAGATA[C/T]
GACATGGTGAGCACTCAAAAGGATAAAATCAACATCACATCACAAAGAACAAATAAGACACTCATAACATAAAAGAAGTGTAGTATAAATAAAGAGCTGC

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	62.80%	37.00%	0.15%	0.00%	NA
All Indica	2759	91.70%	8.00%	0.25%	0.00%	NA
All Japonica	1512	8.10%	91.90%	0.00%	0.00%	NA
Aus	269	95.50%	4.50%	0.00%	0.00%	NA
Indica I	595	95.60%	4.20%	0.17%	0.00%	NA
Indica II	465	97.20%	2.40%	0.43%	0.00%	NA
Indica III	913	90.40%	9.40%	0.22%	0.00%	NA
Indica Intermediate	786	87.20%	12.60%	0.25%	0.00%	NA
Temperate Japonica	767	1.30%	98.70%	0.00%	0.00%	NA
Tropical Japonica	504	19.80%	80.20%	0.00%	0.00%	NA
Japonica Intermediate	241	5.00%	95.00%	0.00%	0.00%	NA
VI/Aromatic	96	13.50%	86.50%	0.00%	0.00%	NA
Intermediate	90	52.20%	47.80%	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
vg0222034653	G -> A	LOC_Os02g36470.1	downstream_gene_variant ; 2956.0bp to feature; MODIFIER	silent_mutation	Average:19.399; most accessible tissue: Minghui63 young leaf, score: 24.836	N	N	N	N
vg0222034653	G -> A	LOC_Os02g36480.1	downstream_gene_variant ; 404.0bp to feature; MODIFIER	silent_mutation	Average:19.399; most accessible tissue: Minghui63 young leaf, score: 24.836	N	N	N	N
vg0222034653	G -> A	LOC_Os02g36490.1	downstream_gene_variant ; 3951.0bp to feature; MODIFIER	silent_mutation	Average:19.399; most accessible tissue: Minghui63 young leaf, score: 24.836	N	N	N	N
vg0222034653	G -> A	LOC_Os02g36490.2	downstream_gene_variant ; 3951.0bp to feature; MODIFIER	silent_mutation	Average:19.399; most accessible tissue: Minghui63 young leaf, score: 24.836	N	N	N	N
vg0222034653	G -> A	LOC_Os02g36490.3	downstream_gene_variant ; 3951.0bp to feature; MODIFIER	silent_mutation	Average:19.399; most accessible tissue: Minghui63 young leaf, score: 24.836	N	N	N	N
vg0222034653	G -> A	LOC_Os02g36480-LOC_Os02g36490	intergenic_region ; MODIFIER	silent_mutation	Average:19.399; most accessible tissue: Minghui63 young leaf, score: 24.836	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0222034653	4.78E-06	4.01E-06	mr1911_2	Jap_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