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Detailed information for vg1116298980:

Variant ID: vg1116298980 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 16298980
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAATATGCCATATGGCTATCTCTAATTAATATTTCTGATAGAAAATATCCCTTTTGCCCTTAATTTGTATACAACTATAAACTAGAAAAAAAACCAAGAT[G/A]
AATAAATAATATTGCAAATATACTTCTCATCATTTCAACATGTGCACATAAAACTTGAGCCTAATGGCTATAGTATACACTTGCAAATACATATTTTTTT

Reverse complement sequence

AAAAAAATATGTATTTGCAAGTGTATACTATAGCCATTAGGCTCAAGTTTTATGTGCACATGTTGAAATGATGAGAAGTATATTTGCAATATTATTTATT[C/T]
ATCTTGGTTTTTTTTCTAGTTTATAGTTGTATACAAATTAAGGGCAAAAGGGATATTTTCTATCAGAAATATTAATTAGAGATAGCCATATGGCATATTA

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	82.50%	17.40%	0.13%	0.00%	NA
All Indica	2759	76.30%	23.50%	0.22%	0.00%	NA
All Japonica	1512	97.20%	2.80%	0.00%	0.00%	NA
Aus	269	57.20%	42.80%	0.00%	0.00%	NA
Indica I	595	77.30%	22.50%	0.17%	0.00%	NA
Indica II	465	93.30%	6.70%	0.00%	0.00%	NA
Indica III	913	60.80%	39.00%	0.22%	0.00%	NA
Indica Intermediate	786	83.50%	16.20%	0.38%	0.00%	NA
Temperate Japonica	767	98.80%	1.20%	0.00%	0.00%	NA
Tropical Japonica	504	94.20%	5.80%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	83.30%	16.70%	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
vg1116298980	G -> A	LOC_Os11g28330.1	downstream_gene_variant ; 2078.0bp to feature; MODIFIER	silent_mutation	Average:39.678; most accessible tissue: Minghui63 panicle, score: 74.563	N	N	N	N
vg1116298980	G -> A	LOC_Os11g28330-LOC_Os11g28340	intergenic_region ; MODIFIER	silent_mutation	Average:39.678; most accessible tissue: Minghui63 panicle, score: 74.563	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1116298980	4.13E-08	NA	mr1758_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