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Detailed information for vg0516367809:

Variant ID: vg0516367809 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 16367809
Reference Allele: C	Alternative Allele: A
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.75, A: 0.25, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

CCATTATGAGATCGAGCTAACTCCTGTCCCAGTCTCTGTTCCAAATTCCCGTGTGGTACCACCTGCCGATTAATTCAGCTATTCCTTTTGTAATTAACTG[C/A]
TGTTACAAAGACAAAAAAACAATATGCACAAATTTGTTTAAATTTTGTACTTTTATATTAGTTTCTTTGTTTTTTTAAAAAAACTTGCTGAGACTGGTTT

Reverse complement sequence

AAACCAGTCTCAGCAAGTTTTTTTAAAAAAACAAAGAAACTAATATAAAAGTACAAAATTTAAACAAATTTGTGCATATTGTTTTTTTGTCTTTGTAACA[G/T]
CAGTTAATTACAAAAGGAATAGCTGAATTAATCGGCAGGTGGTACCACACGGGAATTTGGAACAGAGACTGGGACAGGAGTTAGCTCGATCTCATAATGG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	56.00%	43.50%	0.44%	0.00%	NA
All Indica	2759	78.00%	21.60%	0.40%	0.00%	NA
All Japonica	1512	24.30%	75.40%	0.33%	0.00%	NA
Aus	269	32.00%	68.00%	0.00%	0.00%	NA
Indica I	595	75.30%	24.50%	0.17%	0.00%	NA
Indica II	465	71.00%	28.60%	0.43%	0.00%	NA
Indica III	913	82.40%	17.40%	0.22%	0.00%	NA
Indica Intermediate	786	79.30%	20.00%	0.76%	0.00%	NA
Temperate Japonica	767	7.00%	93.00%	0.00%	0.00%	NA
Tropical Japonica	504	52.80%	46.80%	0.40%	0.00%	NA
Japonica Intermediate	241	19.50%	79.30%	1.24%	0.00%	NA
VI/Aromatic	96	2.10%	95.80%	2.08%	0.00%	NA
Intermediate	90	43.30%	53.30%	3.33%	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
vg0516367809	C -> A	LOC_Os05g28040.1	upstream_gene_variant ; 3798.0bp to feature; MODIFIER	silent_mutation	Average:63.6; most accessible tissue: Callus, score: 88.698	N	N	N	N
vg0516367809	C -> A	LOC_Os05g28040-LOC_Os05g28050	intergenic_region ; MODIFIER	silent_mutation	Average:63.6; most accessible tissue: Callus, score: 88.698	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0516367809	NA	1.02E-14	Grain_width	Jap_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
vg0516367809	NA	1.69E-13	mr1771	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
vg0516367809	NA	9.92E-12	mr1784	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
vg0516367809	5.01E-07	1.66E-07	mr1800	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
vg0516367809	NA	3.79E-09	mr1800	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
vg0516367809	NA	1.34E-06	mr1248_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
vg0516367809	NA	3.64E-06	mr1380_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
vg0516367809	6.43E-06	6.74E-10	mr1380_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
vg0516367809	NA	1.76E-06	mr1423_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
vg0516367809	NA	8.65E-18	mr1540_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
vg0516367809	NA	2.11E-06	mr1561_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
vg0516367809	NA	9.53E-09	mr1561_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
vg0516367809	NA	6.19E-18	mr1732_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
vg0516367809	NA	9.16E-10	mr1771_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
vg0516367809	NA	3.20E-10	mr1784_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
vg0516367809	NA	1.60E-06	mr1875_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
vg0516367809	NA	3.10E-08	mr1875_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
vg0516367809	NA	9.06E-07	mr1908_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
vg0516367809	NA	7.36E-08	mr1908_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
vg0516367809	NA	5.84E-06	mr1977_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
vg0516367809	NA	1.26E-06	mr1996_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