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Detailed information for vg0221853596:

Variant ID: vg0221853596 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 21853596
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 336. )

Flanking Sequence (100 bp) in Reference Genome:

CTTTTTCCCCTGAATCACTGGAAATGCATTTCCTCTTATGTGTGTGTGTGTATGTTTTATCCACTTCACACTGTTTTGCAGGACTGAAAAGAGTAGTTGT[A/G]
TACATTACAAGCAACTTATTTCATACTTACGAGTAAAACGTTGAACGTTTGAATACACTACATGCTTTCTAGACCAAGAATTATTGAGTGATAGACATTA

Reverse complement sequence

TAATGTCTATCACTCAATAATTCTTGGTCTAGAAAGCATGTAGTGTATTCAAACGTTCAACGTTTTACTCGTAAGTATGAAATAAGTTGCTTGTAATGTA[T/C]
ACAACTACTCTTTTCAGTCCTGCAAAACAGTGTGAAGTGGATAAAACATACACACACACACATAAGAGGAAATGCATTTCCAGTGATTCAGGGGAAAAAG

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	97.10%	2.40%	0.47%	0.00%	NA
All Indica	2759	95.20%	4.10%	0.72%	0.00%	NA
All Japonica	1512	99.80%	0.10%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	78.10%	18.70%	3.23%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	96.20%	3.20%	0.64%	0.00%	NA
Temperate Japonica	767	99.70%	0.10%	0.13%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	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	97.80%	1.10%	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
vg0221853596	A -> G	LOC_Os02g36220.1	3_prime_UTR_variant ; 206.0bp to feature; MODIFIER	silent_mutation	Average:31.972; most accessible tissue: Zhenshan97 flower, score: 43.307	N	N	N	N
vg0221853596	A -> G	LOC_Os02g36220.2	3_prime_UTR_variant ; 206.0bp to feature; MODIFIER	silent_mutation	Average:31.972; most accessible tissue: Zhenshan97 flower, score: 43.307	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0221853596	NA	4.61E-06	mr1044	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
vg0221853596	NA	3.07E-07	mr1069	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
vg0221853596	NA	4.00E-07	mr1072	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
vg0221853596	NA	2.48E-06	mr1075	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
vg0221853596	1.31E-06	1.77E-08	mr1076	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
vg0221853596	7.90E-07	NA	mr1077	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
vg0221853596	1.69E-06	1.38E-10	mr1077	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
vg0221853596	NA	1.15E-06	mr1082	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
vg0221853596	NA	6.59E-06	mr1103	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
vg0221853596	NA	4.12E-06	mr1202	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
vg0221853596	NA	4.00E-08	mr1441	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
vg0221853596	NA	3.36E-07	mr1560	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
vg0221853596	NA	3.53E-06	mr1609	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
vg0221853596	NA	5.59E-06	mr1949	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