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Detailed information for vg1108876734:

Variant ID: vg1108876734 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 8876734
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTTACTCCGCTAGGTCTATACCCACACGAGAAGTACGGTTGTACGGGGGTCGTTTCATGCTTAACTTCATGGCTCGGTCCTTAACTGACCAGGGACGGC[G/A]
CTAGCCTTTTCCGAACACCACCCAAGTCCTCCAGCCACCCAGTCGAAAATAGTTGTTTAGTTTCATTTTTCCTTTCACAAATCATGTCACCAATGTCATG

Reverse complement sequence

CATGACATTGGTGACATGATTTGTGAAAGGAAAAATGAAACTAAACAACTATTTTCGACTGGGTGGCTGGAGGACTTGGGTGGTGTTCGGAAAAGGCTAG[C/T]
GCCGTCCCTGGTCAGTTAAGGACCGAGCCATGAAGTTAAGCATGAAACGACCCCCGTACAACCGTACTTCTCGTGTGGGTATAGACCTAGCGGAGTAAAT

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	74.80%	1.20%	22.37%	1.59%	NA
All Indica	2759	60.50%	2.00%	34.94%	2.57%	NA
All Japonica	1512	98.40%	0.00%	1.52%	0.07%	NA
Aus	269	77.00%	1.90%	20.07%	1.12%	NA
Indica I	595	39.30%	1.50%	50.08%	9.08%	NA
Indica II	465	87.50%	1.30%	10.75%	0.43%	NA
Indica III	913	55.20%	3.30%	41.18%	0.33%	NA
Indica Intermediate	786	66.80%	1.10%	30.53%	1.53%	NA
Temperate Japonica	767	98.00%	0.00%	1.83%	0.13%	NA
Tropical Japonica	504	98.60%	0.00%	1.39%	0.00%	NA
Japonica Intermediate	241	99.20%	0.00%	0.83%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	82.20%	0.00%	17.78%	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
vg1108876734	G -> A	LOC_Os11g15640.1	upstream_gene_variant ; 2796.0bp to feature; MODIFIER	silent_mutation	Average:40.957; most accessible tissue: Minghui63 flag leaf, score: 82.975	N	N	N	N
vg1108876734	G -> A	LOC_Os11g15660.1	upstream_gene_variant ; 4059.0bp to feature; MODIFIER	silent_mutation	Average:40.957; most accessible tissue: Minghui63 flag leaf, score: 82.975	N	N	N	N
vg1108876734	G -> A	LOC_Os11g15640-LOC_Os11g15660	intergenic_region ; MODIFIER	silent_mutation	Average:40.957; most accessible tissue: Minghui63 flag leaf, score: 82.975	N	N	N	N
vg1108876734	G -> DEL	N	N	silent_mutation	Average:40.957; most accessible tissue: Minghui63 flag leaf, score: 82.975	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1108876734	1.87E-06	NA	mr1188_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