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Detailed information for vg1107088655:

Variant ID: vg1107088655 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 7088655
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAATTTAGTGTTTAAAATGTTGCTAATTTTTTCTATAAACTTAGTAAAACTTAACAAAGTTTGATTAGAAAAAAGTTAAAACAACTTATGATATAAAACA[G/A]
AGGGAGTATGTACAAAGACAACATGTTAGGGAGGAATTTTTGGAATATATATGAGAGATAGTGAGATGTTTGTCTATGACAAATGTTAATACCGGTGAAA

Reverse complement sequence

TTTCACCGGTATTAACATTTGTCATAGACAAACATCTCACTATCTCTCATATATATTCCAAAAATTCCTCCCTAACATGTTGTCTTTGTACATACTCCCT[C/T]
TGTTTTATATCATAAGTTGTTTTAACTTTTTTCTAATCAAACTTTGTTAAGTTTTACTAAGTTTATAGAAAAAATTAGCAACATTTTAAACACTAAATTA

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	90.40%	7.50%	1.06%	0.97%	NA
All Indica	2759	96.60%	0.10%	1.74%	1.52%	NA
All Japonica	1512	80.80%	19.00%	0.07%	0.07%	NA
Aus	269	95.20%	4.80%	0.00%	0.00%	NA
Indica I	595	99.50%	0.30%	0.17%	0.00%	NA
Indica II	465	88.40%	0.00%	6.67%	4.95%	NA
Indica III	913	99.20%	0.00%	0.22%	0.55%	NA
Indica Intermediate	786	96.20%	0.30%	1.78%	1.78%	NA
Temperate Japonica	767	75.90%	23.90%	0.13%	0.13%	NA
Tropical Japonica	504	86.30%	13.70%	0.00%	0.00%	NA
Japonica Intermediate	241	85.10%	14.90%	0.00%	0.00%	NA
VI/Aromatic	96	54.20%	45.80%	0.00%	0.00%	NA
Intermediate	90	87.80%	7.80%	1.11%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1107088655	G -> A	LOC_Os11g12610.1	upstream_gene_variant ; 3866.0bp to feature; MODIFIER	silent_mutation	Average:23.813; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N
vg1107088655	G -> A	LOC_Os11g12610-LOC_Os11g12620	intergenic_region ; MODIFIER	silent_mutation	Average:23.813; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N
vg1107088655	G -> DEL	N	N	silent_mutation	Average:23.813; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1107088655	NA	6.54E-08	mr1585_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
vg1107088655	NA	8.87E-07	mr1585_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
vg1107088655	8.96E-07	1.46E-08	mr1693_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