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Detailed information for vg1115981616:

Variant ID: vg1115981616 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 15981616
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:

ATGAGATGAAATTGTCTGATTTAACAGCAATCAAGAAAAGACACGATGAACCTGTACTTGAGTATATTCAGAGGTTCAGAGAGATGTGGAATAAGTGCTA[C/T]
AGCTTGAGTTTGACTGATGCCCAGTTAGCCGATTTGGCTTTTCAGGGTATGATTGCTCCGATCAGGGAGAAATTCTCAGCTGAAGACTTTGACAGCTTGT

Reverse complement sequence

ACAAGCTGTCAAAGTCTTCAGCTGAGAATTTCTCCCTGATCGGAGCAATCATACCCTGAAAAGCCAAATCGGCTAACTGGGCATCAGTCAAACTCAAGCT[G/A]
TAGCACTTATTCCACATCTCTCTGAACCTCTGAATATACTCAAGTACAGGTTCATCGTGTCTTTTCTTGATTGCTGTTAAATCAGACAATTTCATCTCAT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	49.70%	23.10%	27.04%	0.15%	NA
All Indica	2759	23.40%	35.80%	40.59%	0.25%	NA
All Japonica	1512	97.80%	0.50%	1.72%	0.00%	NA
Aus	269	33.10%	29.00%	37.92%	0.00%	NA
Indica I	595	19.50%	22.40%	57.65%	0.50%	NA
Indica II	465	18.70%	38.10%	43.23%	0.00%	NA
Indica III	913	26.90%	45.30%	27.60%	0.11%	NA
Indica Intermediate	786	24.90%	33.50%	41.22%	0.38%	NA
Temperate Japonica	767	97.50%	0.30%	2.22%	0.00%	NA
Tropical Japonica	504	97.60%	0.80%	1.59%	0.00%	NA
Japonica Intermediate	241	98.80%	0.80%	0.41%	0.00%	NA
VI/Aromatic	96	92.70%	1.00%	6.25%	0.00%	NA
Intermediate	90	55.60%	17.80%	26.67%	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
vg1115981616	C -> T	LOC_Os11g27760.1	synonymous_variant ; p.Tyr384Tyr; LOW	synonymous_codon	Average:10.492; most accessible tissue: Callus, score: 28.482	N	N	N	N
vg1115981616	C -> DEL	LOC_Os11g27760.1	N	frameshift_variant	Average:10.492; most accessible tissue: Callus, score: 28.482	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1115981616	3.02E-06	NA	mr1151_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
vg1115981616	NA	5.82E-08	mr1299_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1115981616	NA	3.71E-11	mr1537_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1115981616	NA	4.71E-08	mr1727_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1115981616	NA	8.43E-07	mr1785_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1115981616	NA	4.96E-08	mr1804_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1115981616	NA	1.15E-07	mr1837_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
vg1115981616	NA	8.64E-06	mr1840_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1115981616	NA	2.26E-06	mr1915_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251