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Detailed information for vg0202282068:

Variant ID: vg0202282068 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 2282068
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAGTTTTCATAGGTCTGGAGAAACAGTTAGCCGTTATTTCAACAAAGTCCTTCATGCAATCGGTGAGGTACGAGATGAACTAATCAGGCCCCCCTCATTG[G/A]
ACACTCCAACTAAAATAGCAGGAAACCCTAGAAGAGATCCTTACTTTAAGGTCTGAGATTCATCCCTATCTAAATTTATCTTTATGTGAACATTGATATA

Reverse complement sequence

TATATCAATGTTCACATAAAGATAAATTTAGATAGGGATGAATCTCAGACCTTAAAGTAAGGATCTCTTCTAGGGTTTCCTGCTATTTTAGTTGGAGTGT[C/T]
CAATGAGGGGGGCCTGATTAGTTCATCTCGTACCTCACCGATTGCATGAAGGACTTTGTTGAAATAACGGCTAACTGTTTCTCCAGACCTATGAAAACTA

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	81.50%	3.20%	12.04%	3.28%	NA
All Indica	2759	68.50%	5.50%	20.41%	5.55%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	65.70%	4.00%	27.73%	2.52%	NA
Indica II	465	82.40%	0.60%	14.19%	2.80%	NA
Indica III	913	54.40%	11.90%	23.99%	9.64%	NA
Indica Intermediate	786	78.90%	2.00%	14.38%	4.71%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	0.00%	6.67%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0202282068	G -> A	LOC_Os02g04924.1	downstream_gene_variant ; 2225.0bp to feature; MODIFIER	silent_mutation	Average:20.409; most accessible tissue: Callus, score: 43.368	N	N	N	N
vg0202282068	G -> A	LOC_Os02g04924.2	downstream_gene_variant ; 2227.0bp to feature; MODIFIER	silent_mutation	Average:20.409; most accessible tissue: Callus, score: 43.368	N	N	N	N
vg0202282068	G -> A	LOC_Os02g04924-LOC_Os02g04940	intergenic_region ; MODIFIER	silent_mutation	Average:20.409; most accessible tissue: Callus, score: 43.368	N	N	N	N
vg0202282068	G -> DEL	N	N	silent_mutation	Average:20.409; most accessible tissue: Callus, score: 43.368	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0202282068	4.19E-06	7.66E-06	mr1585	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