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Detailed information for vg1114450021:

Variant ID: vg1114450021 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 14450021
Reference Allele: G	Alternative Allele: C
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.83, G: 0.17, others allele: 0.00, population size: 58. )

Flanking Sequence (100 bp) in Reference Genome:

ATGTTAATTGCCACATTAGGTCATTATACATTTAGACTTGTGCTCACTTTTCACACACACACACACTTCACTGGGTTTGGCCTGACCAGGGGCGGTCAGA[G/C]
CAGCCACATAGTGGCGGTCTGACCGGCGCCACAATGGCGGTCTGACCGGCGCATAAGGCCAGTCTGACCGGCAGGACATGCGCGGTCAGACCGGCCCCCT

Reverse complement sequence

AGGGGGCCGGTCTGACCGCGCATGTCCTGCCGGTCAGACTGGCCTTATGCGCCGGTCAGACCGCCATTGTGGCGCCGGTCAGACCGCCACTATGTGGCTG[C/G]
TCTGACCGCCCCTGGTCAGGCCAAACCCAGTGAAGTGTGTGTGTGTGTGAAAAGTGAGCACAAGTCTAAATGTATAATGACCTAATGTGGCAATTAACAT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	64.00%	35.60%	0.36%	0.00%	NA
All Indica	2759	96.20%	3.50%	0.33%	0.00%	NA
All Japonica	1512	3.10%	96.70%	0.20%	0.00%	NA
Aus	269	98.50%	1.10%	0.37%	0.00%	NA
Indica I	595	93.10%	6.40%	0.50%	0.00%	NA
Indica II	465	98.50%	1.50%	0.00%	0.00%	NA
Indica III	913	99.20%	0.80%	0.00%	0.00%	NA
Indica Intermediate	786	93.60%	5.60%	0.76%	0.00%	NA
Temperate Japonica	767	3.00%	96.60%	0.39%	0.00%	NA
Tropical Japonica	504	3.80%	96.20%	0.00%	0.00%	NA
Japonica Intermediate	241	2.10%	97.90%	0.00%	0.00%	NA
VI/Aromatic	96	9.40%	86.50%	4.17%	0.00%	NA
Intermediate	90	56.70%	43.30%	0.00%	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
vg1114450021	G -> C	LOC_Os11g25360.1	downstream_gene_variant ; 3169.0bp to feature; MODIFIER	silent_mutation	Average:43.567; most accessible tissue: Minghui63 young leaf, score: 72.959	N	N	N	N
vg1114450021	G -> C	LOC_Os11g25350.1	intron_variant ; MODIFIER	silent_mutation	Average:43.567; most accessible tissue: Minghui63 young leaf, score: 72.959	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1114450021	NA	1.32E-18	Yield	All	Not	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
vg1114450021	NA	2.67E-19	mr1021	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
vg1114450021	NA	1.31E-74	mr1135	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
vg1114450021	NA	3.65E-22	mr1168	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
vg1114450021	NA	1.52E-09	mr1336	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
vg1114450021	NA	2.50E-25	mr1383	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
vg1114450021	NA	6.55E-13	mr1701	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
vg1114450021	2.78E-07	NA	mr1719	Jap_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
vg1114450021	3.03E-07	2.17E-106	mr1758	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
vg1114450021	NA	4.06E-06	mr1020_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
vg1114450021	NA	6.59E-20	mr1168_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
vg1114450021	NA	1.35E-07	mr1335_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
vg1114450021	7.51E-07	5.06E-151	mr1758_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
vg1114450021	NA	3.68E-09	mr1835_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
vg1114450021	NA	1.04E-21	mr1971_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