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Detailed information for vg0134539333:

Variant ID: vg0134539333 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 34539333
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:

TGAAAAGGCATAGTCTTTCTGTTTATCCTTAAAAAAATGTTTGACCCCTCCTGTCAGACTATTGATATACCTGGTAGAGAGCCAGCAAAGCCATTGTTTA[G/T]
TGCGATGTTTGAATTAAATTGTGCAACATTGTAATAGAGTTTTTCTCTTATCCTAGGGTTGTATTTTTCTCCCGTTATATTTAATGAAAAGGCACAATCA

Reverse complement sequence

TGATTGTGCCTTTTCATTAAATATAACGGGAGAAAAATACAACCCTAGGATAAGAGAAAAACTCTATTACAATGTTGCACAATTTAATTCAAACATCGCA[C/A]
TAAACAATGGCTTTGCTGGCTCTCTACCAGGTATATCAATAGTCTGACAGGAGGGGTCAAACATTTTTTTAAGGATAAACAGAAAGACTATGCCTTTTCA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	81.10%	7.60%	0.99%	10.30%	NA
All Indica	2759	99.70%	0.00%	0.07%	0.18%	NA
All Japonica	1512	48.70%	22.80%	2.71%	25.79%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.80%	0.00%	0.00%	0.22%	NA
Indica Intermediate	786	99.50%	0.00%	0.13%	0.38%	NA
Temperate Japonica	767	57.10%	32.60%	4.69%	5.61%	NA
Tropical Japonica	504	49.60%	7.10%	0.20%	43.06%	NA
Japonica Intermediate	241	19.90%	24.50%	1.66%	53.94%	NA
VI/Aromatic	96	15.60%	0.00%	2.08%	82.29%	NA
Intermediate	90	71.10%	12.20%	2.22%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0134539333	G -> T	LOC_Os01g59700.1	downstream_gene_variant ; 1887.0bp to feature; MODIFIER	silent_mutation	Average:44.743; most accessible tissue: Minghui63 flower, score: 68.878	N	N	N	N
vg0134539333	G -> T	LOC_Os01g59700-LOC_Os01g59710	intergenic_region ; MODIFIER	silent_mutation	Average:44.743; most accessible tissue: Minghui63 flower, score: 68.878	N	N	N	N
vg0134539333	G -> DEL	N	N	silent_mutation	Average:44.743; most accessible tissue: Minghui63 flower, score: 68.878	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0134539333	1.05E-06	NA	mr1070	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
vg0134539333	NA	2.41E-07	mr1070	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
vg0134539333	1.81E-07	NA	mr1097	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
vg0134539333	NA	1.73E-07	mr1097	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
vg0134539333	3.29E-06	NA	mr1154	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
vg0134539333	NA	1.22E-06	mr1154	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
vg0134539333	NA	1.07E-06	mr1252	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
vg0134539333	NA	3.50E-06	mr1872	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