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Detailed information for vg1115159539:

Variant ID: vg1115159539 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 15159539
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATAAATGCAATTAATAATCGGAATTAGCGTGGTGGAATTTTTTCTTGAGTTCCCCATGCTCCAGTGCATTAACAAGATTTTTAGTGGAATTTTCAGAGCC[T/A]
TGGAAATAATTTTAACCAACTAAAAATCACCAAAGTGCAATTTTAAATCCCAGGAAAAATCCTTTCTTCTTTTTCTTTTTCTTTTCCTTCATTTTTCCCT

Reverse complement sequence

AGGGAAAAATGAAGGAAAAGAAAAAGAAAAAGAAGAAAGGATTTTTCCTGGGATTTAAAATTGCACTTTGGTGATTTTTAGTTGGTTAAAATTATTTCCA[A/T]
GGCTCTGAAAATTCCACTAAAAATCTTGTTAATGCACTGGAGCATGGGGAACTCAAGAAAAAATTCCACCACGCTAATTCCGATTATTAATTGCATTTAT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.80%	2.50%	2.79%	0.95%	NA
All Indica	2759	91.80%	2.90%	3.77%	1.59%	NA
All Japonica	1512	97.50%	1.30%	1.12%	0.07%	NA
Aus	269	92.90%	5.20%	1.86%	0.00%	NA
Indica I	595	93.80%	1.80%	3.87%	0.50%	NA
Indica II	465	90.50%	0.90%	4.30%	4.30%	NA
Indica III	913	91.60%	4.80%	2.96%	0.66%	NA
Indica Intermediate	786	91.20%	2.50%	4.33%	1.91%	NA
Temperate Japonica	767	99.20%	0.00%	0.65%	0.13%	NA
Tropical Japonica	504	97.20%	1.60%	1.19%	0.00%	NA
Japonica Intermediate	241	92.50%	5.00%	2.49%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	91.10%	2.20%	6.67%	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
vg1115159539	T -> A	LOC_Os11g26460.1	downstream_gene_variant ; 220.0bp to feature; MODIFIER	silent_mutation	Average:15.928; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N
vg1115159539	T -> A	LOC_Os11g26460-LOC_Os11g26470	intergenic_region ; MODIFIER	silent_mutation	Average:15.928; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N
vg1115159539	T -> DEL	N	N	silent_mutation	Average:15.928; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1115159539	3.08E-07	5.57E-09	mr1695_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