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Detailed information for vg0202692022:

Variant ID: vg0202692022 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 2692022
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.02, others allele: 0.00, population size: 55. )

Flanking Sequence (100 bp) in Reference Genome:

TATTTGGTAGTGGTAGGTTTAGGTAGTATAATACCTAGGGTTTAGTTATATGGGAGTCGATTGTGGAGTAGGATAGCATATCGGCTAGGCTCTATATTTT[G/A]
TGTGGAGGTTCTAGAGGATTGGTGGCTAGAGGGGATTAAGCAACTACTGTCGCTTATATTTTATGCGAAGGCTCTCATGGTTTGGACGATAGGAAAAATA

Reverse complement sequence

TATTTTTCCTATCGTCCAAACCATGAGAGCCTTCGCATAAAATATAAGCGACAGTAGTTGCTTAATCCCCTCTAGCCACCAATCCTCTAGAACCTCCACA[C/T]
AAAATATAGAGCCTAGCCGATATGCTATCCTACTCCACAATCGACTCCCATATAACTAAACCCTAGGTATTATACTACCTAAACCTACCACTACCAAATA

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	41.60%	5.90%	8.13%	44.33%	NA
All Indica	2759	10.90%	7.20%	11.42%	70.46%	NA
All Japonica	1512	96.40%	0.10%	0.20%	3.37%	NA
Aus	269	20.10%	27.90%	22.68%	29.37%	NA
Indica I	595	13.10%	0.80%	11.09%	74.96%	NA
Indica II	465	4.50%	13.30%	10.54%	71.61%	NA
Indica III	913	11.60%	6.20%	13.69%	68.46%	NA
Indica Intermediate	786	12.20%	9.50%	9.54%	68.70%	NA
Temperate Japonica	767	95.60%	0.10%	0.26%	4.04%	NA
Tropical Japonica	504	97.80%	0.00%	0.00%	2.18%	NA
Japonica Intermediate	241	95.90%	0.00%	0.41%	3.73%	NA
VI/Aromatic	96	96.90%	2.10%	0.00%	1.04%	NA
Intermediate	90	70.00%	2.20%	5.56%	22.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0202692022	G -> A	LOC_Os02g05560.1	upstream_gene_variant ; 3667.0bp to feature; MODIFIER	silent_mutation	Average:33.294; most accessible tissue: Callus, score: 55.755	N	N	N	N
vg0202692022	G -> A	LOC_Os02g05550-LOC_Os02g05560	intergenic_region ; MODIFIER	silent_mutation	Average:33.294; most accessible tissue: Callus, score: 55.755	N	N	N	N
vg0202692022	G -> DEL	N	N	silent_mutation	Average:33.294; most accessible tissue: Callus, score: 55.755	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0202692022	NA	8.74E-06	mr1177	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
vg0202692022	NA	1.01E-08	mr1180	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
vg0202692022	NA	2.30E-08	mr1183	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
vg0202692022	NA	4.55E-09	mr1503	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
vg0202692022	NA	2.43E-07	mr1180_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