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Detailed information for vg1105749725:

Variant ID: vg1105749725 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 5749725
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.84, A: 0.15, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

AACAAACACTTATTGTACGTGCAAAGTTGTCCAAAAAAGTAATGCTACTATCATAATATCACAAACTAGATTTTATAAATTTTTATAATATAAAATGATG[G/A]
TAAAATTTCTAAAATGTCTGTCCGAATCTTATCTTATAACATTAAATATTTATGATTACAGGGAATATAAGTTTTGTTATCTTTGCATGGCACTAAACTT

Reverse complement sequence

AAGTTTAGTGCCATGCAAAGATAACAAAACTTATATTCCCTGTAATCATAAATATTTAATGTTATAAGATAAGATTCGGACAGACATTTTAGAAATTTTA[C/T]
CATCATTTTATATTATAAAAATTTATAAAATCTAGTTTGTGATATTATGATAGTAGCATTACTTTTTTGGACAACTTTGCACGTACAATAAGTGTTTGTT

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	59.60%	40.20%	0.19%	0.00%	NA
All Indica	2759	45.90%	53.90%	0.25%	0.00%	NA
All Japonica	1512	91.10%	8.90%	0.07%	0.00%	NA
Aus	269	7.10%	92.90%	0.00%	0.00%	NA
Indica I	595	17.00%	82.50%	0.50%	0.00%	NA
Indica II	465	69.50%	30.50%	0.00%	0.00%	NA
Indica III	913	51.90%	47.80%	0.33%	0.00%	NA
Indica Intermediate	786	46.80%	53.10%	0.13%	0.00%	NA
Temperate Japonica	767	94.00%	5.90%	0.13%	0.00%	NA
Tropical Japonica	504	85.10%	14.90%	0.00%	0.00%	NA
Japonica Intermediate	241	94.20%	5.80%	0.00%	0.00%	NA
VI/Aromatic	96	94.80%	5.20%	0.00%	0.00%	NA
Intermediate	90	71.10%	27.80%	1.11%	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
vg1105749725	G -> A	LOC_Os11g10510.1	upstream_gene_variant ; 1573.0bp to feature; MODIFIER	silent_mutation	Average:30.902; most accessible tissue: Callus, score: 62.86	N	N	N	N
vg1105749725	G -> A	LOC_Os11g10510.2	upstream_gene_variant ; 1573.0bp to feature; MODIFIER	silent_mutation	Average:30.902; most accessible tissue: Callus, score: 62.86	N	N	N	N
vg1105749725	G -> A	LOC_Os11g10510-LOC_Os11g10520	intergenic_region ; MODIFIER	silent_mutation	Average:30.902; most accessible tissue: Callus, score: 62.86	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1105749725	5.17E-07	1.54E-07	mr1211	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
vg1105749725	NA	1.39E-08	mr1607	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
vg1105749725	NA	1.30E-07	mr1680	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