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Detailed information for vg1106670681:

Variant ID: vg1106670681 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 6670681
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAATCATGCGTAGAGAACGTGCATGTGGTGTTTGTTGAGCGCAGGGTTTACGATTCTAAAATGACCTTCCGTTTCAAGCTCGGGCGGAACGACGGTTTTC[G/A]
CAAAATCAGGTGGAATGCAGTAGATTCCGAATAAATTTCATAATCAAAATTTGAAAACAAATTTCCTTAGTTTACTGATAAGCTCGCGAAAATCGGTCGG

Reverse complement sequence

CCGACCGATTTTCGCGAGCTTATCAGTAAACTAAGGAAATTTGTTTTCAAATTTTGATTATGAAATTTATTCGGAATCTACTGCATTCCACCTGATTTTG[C/T]
GAAAACCGTCGTTCCGCCCGAGCTTGAAACGGAAGGTCATTTTAGAATCGTAAACCCTGCGCTCAACAAACACCACATGCACGTTCTCTACGCATGATTT

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	56.60%	7.20%	1.04%	35.23%	NA
All Indica	2759	37.90%	11.30%	0.54%	50.24%	NA
All Japonica	1512	81.80%	1.30%	1.98%	14.95%	NA
Aus	269	93.30%	0.00%	0.74%	5.95%	NA
Indica I	595	18.30%	7.70%	0.34%	73.61%	NA
Indica II	465	26.00%	3.70%	0.86%	69.46%	NA
Indica III	913	55.80%	15.80%	0.22%	28.26%	NA
Indica Intermediate	786	39.10%	13.40%	0.89%	46.69%	NA
Temperate Japonica	767	90.90%	2.00%	3.39%	3.78%	NA
Tropical Japonica	504	70.40%	0.80%	0.00%	28.77%	NA
Japonica Intermediate	241	76.80%	0.00%	1.66%	21.58%	NA
VI/Aromatic	96	88.50%	0.00%	1.04%	10.42%	NA
Intermediate	90	60.00%	8.90%	1.11%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1106670681	G -> A	LOC_Os11g12000.1	intron_variant ; MODIFIER	silent_mutation	Average:13.925; most accessible tissue: Callus, score: 78.644	N	N	N	N
vg1106670681	G -> DEL	N	N	silent_mutation	Average:13.925; most accessible tissue: Callus, score: 78.644	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1106670681	3.50E-06	5.93E-07	mr1781	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