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Detailed information for vg1115719147:

Variant ID: vg1115719147 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 15719147
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACAATCCATCAAATCAACGGTTAGATCTTTCTGATTAACGTGAGAGCTTCTAAAAAGTGCCCGATTAGTATAGGTATAGATAGATAGATTTCACCCTATT[G/A]
GATGTATCAGGAGGTACCACATTTACCATTTAGTAACTAGCAGCTAATAGGAGGTAGCGAATTCTGCAACAAAAATATTCTGGTACTGTTTGAAATGCTG

Reverse complement sequence

CAGCATTTCAAACAGTACCAGAATATTTTTGTTGCAGAATTCGCTACCTCCTATTAGCTGCTAGTTACTAAATGGTAAATGTGGTACCTCCTGATACATC[C/T]
AATAGGGTGAAATCTATCTATCTATACCTATACTAATCGGGCACTTTTTAGAAGCTCTCACGTTAATCAGAAAGATCTAACCGTTGATTTGATGGATTGT

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	96.20%	2.70%	1.06%	0.00%	NA
All Indica	2759	99.90%	0.00%	0.11%	0.00%	NA
All Japonica	1512	88.40%	8.50%	3.11%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.60%	0.00%	0.38%	0.00%	NA
Temperate Japonica	767	78.40%	16.00%	5.61%	0.00%	NA
Tropical Japonica	504	99.60%	0.20%	0.20%	0.00%	NA
Japonica Intermediate	241	97.10%	1.70%	1.24%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	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
vg1115719147	G -> A	LOC_Os11g27329.2	downstream_gene_variant ; 3605.0bp to feature; MODIFIER	silent_mutation	Average:60.704; most accessible tissue: Minghui63 root, score: 84.447	N	N	N	N
vg1115719147	G -> A	LOC_Os11g27329.6	downstream_gene_variant ; 3605.0bp to feature; MODIFIER	silent_mutation	Average:60.704; most accessible tissue: Minghui63 root, score: 84.447	N	N	N	N
vg1115719147	G -> A	LOC_Os11g27329.1	intron_variant ; MODIFIER	silent_mutation	Average:60.704; most accessible tissue: Minghui63 root, score: 84.447	N	N	N	N
vg1115719147	G -> A	LOC_Os11g27329.5	intron_variant ; MODIFIER	silent_mutation	Average:60.704; most accessible tissue: Minghui63 root, score: 84.447	N	N	N	N
vg1115719147	G -> A	LOC_Os11g27329.4	intron_variant ; MODIFIER	silent_mutation	Average:60.704; most accessible tissue: Minghui63 root, score: 84.447	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1115719147	9.90E-07	NA	mr1768_2	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