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Detailed information for vg1125085953:

Variant ID: vg1125085953 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25085953
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTCAGAGGTGAGGTTTACTCACCTCAAACGGCTTTAAGTCCCAGCCCGTTTGAGATGACTTCTGCCACTGTATATATATATATATGTCTTCTCTCCCAGC[G/A]
GGGCCCACATGAGGAGATAAGGTCGGCCGGCTCCCTCTTCTCCACTTCTCCTCTATCTCTTCCACTTCTTCTCTATCTCTCCTCTCTTTCTCTATGCCGT

Reverse complement sequence

ACGGCATAGAGAAAGAGAGGAGAGATAGAGAAGAAGTGGAAGAGATAGAGGAGAAGTGGAGAAGAGGGAGCCGGCCGACCTTATCTCCTCATGTGGGCCC[C/T]
GCTGGGAGAGAAGACATATATATATATATACAGTGGCAGAAGTCATCTCAAACGGGCTGGGACTTAAAGCCGTTTGAGGTGAGTAAACCTCACCTCTGAC

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	86.60%	1.50%	7.79%	4.10%	NA
All Indica	2759	97.50%	0.80%	1.41%	0.33%	NA
All Japonica	1512	69.50%	1.30%	17.39%	11.77%	NA
Aus	269	73.60%	9.70%	14.87%	1.86%	NA
Indica I	595	97.80%	0.50%	0.84%	0.84%	NA
Indica II	465	98.50%	0.00%	1.29%	0.22%	NA
Indica III	913	96.70%	1.10%	2.08%	0.11%	NA
Indica Intermediate	786	97.50%	1.10%	1.15%	0.25%	NA
Temperate Japonica	767	72.20%	0.70%	7.69%	19.43%	NA
Tropical Japonica	504	68.50%	2.60%	27.38%	1.59%	NA
Japonica Intermediate	241	63.10%	0.80%	27.39%	8.71%	NA
VI/Aromatic	96	76.00%	3.10%	19.79%	1.04%	NA
Intermediate	90	88.90%	2.20%	7.78%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1125085953	G -> A	LOC_Os11g41760-LOC_Os11g41770	intergenic_region ; MODIFIER	silent_mutation	Average:55.342; most accessible tissue: Zhenshan97 flag leaf, score: 76.925	N	N	N	N
vg1125085953	G -> DEL	N	N	silent_mutation	Average:55.342; most accessible tissue: Zhenshan97 flag leaf, score: 76.925	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125085953	NA	8.19E-06	mr1063	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
vg1125085953	NA	3.47E-06	mr1180	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
vg1125085953	1.92E-11	NA	mr1238	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
vg1125085953	NA	1.48E-06	mr1238	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
vg1125085953	2.71E-09	NA	mr1309	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
vg1125085953	1.31E-07	NA	mr1484	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
vg1125085953	NA	3.25E-06	mr1484	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
vg1125085953	NA	4.26E-07	mr1723	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
vg1125085953	1.18E-11	NA	mr1841	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
vg1125085953	NA	2.57E-06	mr1841	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
vg1125085953	1.12E-10	5.89E-17	mr1900	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
vg1125085953	NA	8.70E-08	mr1900	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
vg1125085953	1.71E-08	2.32E-07	mr1925	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
vg1125085953	3.46E-06	NA	mr1925	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
vg1125085953	NA	2.30E-06	mr1063_2	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
vg1125085953	6.91E-10	NA	mr1238_2	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
vg1125085953	1.09E-08	NA	mr1484_2	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
vg1125085953	5.46E-06	NA	mr1609_2	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
vg1125085953	NA	4.73E-06	mr1723_2	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
vg1125085953	9.24E-10	NA	mr1841_2	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
vg1125085953	2.57E-08	NA	mr1900_2	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
vg1125085953	3.61E-09	2.55E-08	mr1925_2	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
vg1125085953	2.97E-06	NA	mr1945_2	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
vg1125085953	NA	2.66E-07	mr1966_2	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