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Detailed information for vg0626134561:

Variant ID: vg0626134561 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 26134561
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.89, A: 0.11, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:

GTCTTCTTGATCCTAACCTAAAGTAAAGGGATTGGCAACGTACAAAAAAAATATCAAGGACCTAAAAGGAGGTACACAACGATTTTTTTTTAAAAAAGGC[G/A]
AAAATTAGAGAAAGAACTTATCTCTACTATTATAAAAATTGAATATCTTTTTGCCAGTACTTTAGCACTGTCAACGAGAAATCTCATAAACCGGATGAAT

Reverse complement sequence

ATTCATCCGGTTTATGAGATTTCTCGTTGACAGTGCTAAAGTACTGGCAAAAAGATATTCAATTTTTATAATAGTAGAGATAAGTTCTTTCTCTAATTTT[C/T]
GCCTTTTTTAAAAAAAAATCGTTGTGTACCTCCTTTTAGGTCCTTGATATTTTTTTTGTACGTTGCCAATCCCTTTACTTTAGGTTAGGATCAAGAAGAC

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	84.70%	14.90%	0.40%	0.00%	NA
All Indica	2759	97.80%	2.20%	0.00%	0.00%	NA
All Japonica	1512	57.50%	41.30%	1.26%	0.00%	NA
Aus	269	98.50%	1.50%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	95.50%	4.50%	0.00%	0.00%	NA
Indica III	913	99.50%	0.50%	0.00%	0.00%	NA
Indica Intermediate	786	95.70%	4.30%	0.00%	0.00%	NA
Temperate Japonica	767	74.80%	23.30%	1.83%	0.00%	NA
Tropical Japonica	504	25.80%	74.00%	0.20%	0.00%	NA
Japonica Intermediate	241	68.50%	29.90%	1.66%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	83.30%	16.70%	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
vg0626134561	G -> A	LOC_Os06g43480.1	upstream_gene_variant ; 2468.0bp to feature; MODIFIER	silent_mutation	Average:31.909; most accessible tissue: Callus, score: 61.884	N	N	N	N
vg0626134561	G -> A	LOC_Os06g43470-LOC_Os06g43480	intergenic_region ; MODIFIER	silent_mutation	Average:31.909; most accessible tissue: Callus, score: 61.884	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0626134561	9.58E-06	NA	Awn_length	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
vg0626134561	NA	1.11E-09	Heading_date	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
vg0626134561	NA	1.91E-08	mr1002	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
vg0626134561	NA	3.36E-06	mr1028	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
vg0626134561	NA	5.03E-07	mr1338	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
vg0626134561	NA	1.16E-13	mr1449	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
vg0626134561	NA	1.05E-06	mr1652	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
vg0626134561	NA	3.20E-07	mr1797	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
vg0626134561	NA	3.20E-07	mr1801	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
vg0626134561	NA	5.68E-06	mr1991	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
vg0626134561	NA	1.32E-11	mr1097_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
vg0626134561	NA	6.22E-06	mr1330_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
vg0626134561	NA	3.20E-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
vg0626134561	NA	5.50E-09	mr1449_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
vg0626134561	NA	9.44E-08	mr1696_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