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Detailed information for vg1125009726:

Variant ID: vg1125009726 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25009726
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

CATACATAAAGTATTAGATATAAAAAAAAAATAATTACACAGATTGCGTCTAAATTGCGAGATGAATCTTTTAAACCCAATTGCTCCAAGATTTGACAAT[G/A]
TGGTGCTATAGCAAACATTTGCTAATGACGGATTAATTAGGCTTAATAAATTCGTCTTGCAGTTTACAGGCGGATTCTGTAATTTATTTGGTTATTAATT

Reverse complement sequence

AATTAATAACCAAATAAATTACAGAATCCGCCTGTAAACTGCAAGACGAATTTATTAAGCCTAATTAATCCGTCATTAGCAAATGTTTGCTATAGCACCA[C/T]
ATTGTCAAATCTTGGAGCAATTGGGTTTAAAAGATTCATCTCGCAATTTAGACGCAATCTGTGTAATTATTTTTTTTTTATATCTAATACTTTATGTATG

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	84.60%	10.40%	1.59%	3.43%	NA
All Indica	2759	86.40%	9.70%	0.65%	3.23%	NA
All Japonica	1512	85.00%	11.20%	3.57%	0.20%	NA
Aus	269	81.40%	0.70%	0.74%	17.10%	NA
Indica I	595	98.00%	0.80%	1.18%	0.00%	NA
Indica II	465	72.50%	17.60%	0.86%	9.03%	NA
Indica III	913	90.70%	9.00%	0.11%	0.22%	NA
Indica Intermediate	786	80.80%	12.70%	0.76%	5.73%	NA
Temperate Japonica	767	93.50%	0.70%	5.61%	0.26%	NA
Tropical Japonica	504	68.80%	30.00%	1.19%	0.00%	NA
Japonica Intermediate	241	91.70%	5.80%	2.07%	0.41%	NA
VI/Aromatic	96	35.40%	44.80%	0.00%	19.79%	NA
Intermediate	90	85.60%	7.80%	1.11%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1125009726	G -> A	LOC_Os11g41670.1	upstream_gene_variant ; 390.0bp to feature; MODIFIER	silent_mutation	Average:41.108; most accessible tissue: Minghui63 root, score: 57.225	N	N	N	N
vg1125009726	G -> A	LOC_Os11g41670-LOC_Os11g41680	intergenic_region ; MODIFIER	silent_mutation	Average:41.108; most accessible tissue: Minghui63 root, score: 57.225	N	N	N	N
vg1125009726	G -> DEL	N	N	silent_mutation	Average:41.108; most accessible tissue: Minghui63 root, score: 57.225	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125009726	NA	4.32E-06	mr1138	Jap_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
vg1125009726	9.28E-07	NA	mr1609	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
vg1125009726	NA	2.90E-08	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
vg1125009726	NA	5.39E-07	mr1696	Jap_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
vg1125009726	NA	1.90E-06	mr1830	Jap_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
vg1125009726	NA	1.62E-09	mr1609_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
vg1125009726	NA	3.82E-06	mr1795_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