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Detailed information for vg1104740558:

Variant ID: vg1104740558 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 4740558
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, A: 0.05, others allele: 0.00, population size: 38. )

Flanking Sequence (100 bp) in Reference Genome:

CTGTGGACCAGACACGGTCATGTTCAGTTGGCAGTTGGCTACTTCGATCTCGTAGTAGTATATGTTTTTTTCTATCCGGATAAAAATTTATACCATGTTA[C/A]
ATCGAATGTTTGGATACATGCATAGAGGATTAAATATAAATGAAAAAATAACTAATTACATAAACTGTGTGTAAATTGCGAGACGAATCTTTTAAGCCTA

Reverse complement sequence

TAGGCTTAAAAGATTCGTCTCGCAATTTACACACAGTTTATGTAATTAGTTATTTTTTCATTTATATTTAATCCTCTATGCATGTATCCAAACATTCGAT[G/T]
TAACATGGTATAAATTTTTATCCGGATAGAAAAAAACATATACTACTACGAGATCGAAGTAGCCAACTGCCAACTGAACATGACCGTGTCTGGTCCACAG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	33.20%	15.60%	0.78%	50.42%	NA
All Indica	2759	6.70%	14.20%	0.33%	78.72%	NA
All Japonica	1512	84.30%	8.60%	1.79%	5.36%	NA
Aus	269	0.00%	71.00%	0.00%	29.00%	NA
Indica I	595	1.80%	41.70%	0.84%	55.63%	NA
Indica II	465	4.30%	3.90%	0.22%	91.61%	NA
Indica III	913	9.60%	6.10%	0.11%	84.12%	NA
Indica Intermediate	786	8.50%	8.90%	0.25%	82.32%	NA
Temperate Japonica	767	85.30%	10.30%	3.39%	1.04%	NA
Tropical Japonica	504	82.50%	4.40%	0.00%	13.10%	NA
Japonica Intermediate	241	84.60%	12.00%	0.41%	2.90%	NA
VI/Aromatic	96	70.80%	12.50%	0.00%	16.67%	NA
Intermediate	90	45.60%	13.30%	1.11%	40.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1104740558	C -> A	LOC_Os11g08950.1	upstream_gene_variant ; 1761.0bp to feature; MODIFIER	silent_mutation	Average:70.19; most accessible tissue: Minghui63 root, score: 86.792	N	N	N	N
vg1104740558	C -> A	LOC_Os11g08950-LOC_Os11g08970	intergenic_region ; MODIFIER	silent_mutation	Average:70.19; most accessible tissue: Minghui63 root, score: 86.792	N	N	N	N
vg1104740558	C -> DEL	N	N	silent_mutation	Average:70.19; most accessible tissue: Minghui63 root, score: 86.792	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1104740558	1.96E-08	6.31E-19	Awn_length	Jap_All	YES	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1104740558	NA	9.92E-09	mr1201	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
vg1104740558	NA	1.76E-07	mr1201	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
vg1104740558	NA	4.27E-07	mr1201	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
vg1104740558	NA	6.64E-07	mr1219	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
vg1104740558	NA	3.73E-06	mr1219	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
vg1104740558	NA	2.65E-11	mr1274	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
vg1104740558	NA	5.83E-12	mr1274	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
vg1104740558	NA	3.86E-06	mr1274	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
vg1104740558	NA	4.23E-06	mr1406	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
vg1104740558	8.69E-06	8.69E-06	mr1487	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
vg1104740558	1.69E-06	7.12E-09	mr1638	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
vg1104740558	NA	1.47E-07	mr1933	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
vg1104740558	NA	5.14E-07	mr1201_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
vg1104740558	NA	5.07E-07	mr1219_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
vg1104740558	NA	1.21E-08	mr1274_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
vg1104740558	NA	1.04E-07	mr1274_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
vg1104740558	NA	8.38E-07	mr1608_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