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Detailed information for vg0117665352:

Variant ID: vg0117665352 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 17665352
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:

TGAATTTTCATTGGTACACAGAGAATTTACTCATAGCAAAGCGCTAGTGACTGACCTGTCTCTCCCCCATGTCAGGCAATGGAAAGCAAGGAGCGATGTT[G/A]
TATGAAATGGATTGCTTCAATGCATAGGTTTTTTTTGAAACAAACCCGAAAACATAAGCTAGATATTGTGATATTTACTTTATATTATCCTCTGGAGTAT

Reverse complement sequence

ATACTCCAGAGGATAATATAAAGTAAATATCACAATATCTAGCTTATGTTTTCGGGTTTGTTTCAAAAAAAACCTATGCATTGAAGCAATCCATTTCATA[C/T]
AACATCGCTCCTTGCTTTCCATTGCCTGACATGGGGGAGAGACAGGTCAGTCACTAGCGCTTTGCTATGAGTAAATTCTCTGTGTACCAATGAAAATTCA

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	81.00%	18.80%	0.13%	0.00%	NA
All Indica	2759	70.90%	28.90%	0.22%	0.00%	NA
All Japonica	1512	97.70%	2.30%	0.00%	0.00%	NA
Aus	269	80.70%	19.30%	0.00%	0.00%	NA
Indica I	595	62.40%	37.30%	0.34%	0.00%	NA
Indica II	465	95.30%	4.70%	0.00%	0.00%	NA
Indica III	913	60.40%	39.40%	0.22%	0.00%	NA
Indica Intermediate	786	75.20%	24.60%	0.25%	0.00%	NA
Temperate Japonica	767	99.10%	0.90%	0.00%	0.00%	NA
Tropical Japonica	504	95.00%	5.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	6.70%	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
vg0117665352	G -> A	LOC_Os01g32250.1	upstream_gene_variant ; 1835.0bp to feature; MODIFIER	silent_mutation	Average:56.622; most accessible tissue: Minghui63 root, score: 71.259	N	N	N	N
vg0117665352	G -> A	LOC_Os01g32230-LOC_Os01g32250	intergenic_region ; MODIFIER	silent_mutation	Average:56.622; most accessible tissue: Minghui63 root, score: 71.259	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0117665352	4.75E-07	NA	mr1519	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
vg0117665352	8.03E-07	9.75E-09	mr1519	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
vg0117665352	NA	4.16E-06	mr1105_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
vg0117665352	NA	9.29E-08	mr1218_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
vg0117665352	NA	2.96E-07	mr1232_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
vg0117665352	4.23E-12	NA	mr1519_2	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
vg0117665352	4.70E-12	1.99E-20	mr1519_2	Ind_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
vg0117665352	NA	4.04E-06	mr1874_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
vg0117665352	NA	2.42E-06	mr1901_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