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Detailed information for vg1116386156:

Variant ID: vg1116386156 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 16386156
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, G: 0.06, others allele: 0.00, population size: 168. )

Flanking Sequence (100 bp) in Reference Genome:

CTGCATGCTCCTCTAGAATGCTAGAACCTGAACCAAAGGCAAGTGACCTGAAGAAGTACCAGTATTCCTCTTGGAGTAATGGATCGATCCGCATCGCTCC[C/G]
GTCGTACCAAGATCTTTGATGTTGTCATTCTCGCTGACTATTATGATCTTGCTTCCATTTCCAATTGATCTTAGAGAAGCACAGAGTGTAGCCCATGCTA

Reverse complement sequence

TAGCATGGGCTACACTCTGTGCTTCTCTAAGATCAATTGGAAATGGAAGCAAGATCATAATAGTCAGCGAGAATGACAACATCAAAGATCTTGGTACGAC[G/C]
GGAGCGATGCGGATCGATCCATTACTCCAAGAGGAATACTGGTACTTCTTCAGGTCACTTGCCTTTGGTTCAGGTTCTAGCATTCTAGAGGAGCATGCAG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	18.80%	7.30%	0.99%	72.89%	NA
All Indica	2759	8.90%	0.30%	1.38%	89.42%	NA
All Japonica	1512	38.50%	18.40%	0.53%	42.59%	NA
Aus	269	0.40%	2.60%	0.00%	97.03%	NA
Indica I	595	10.10%	0.20%	1.18%	88.57%	NA
Indica II	465	4.90%	0.20%	1.94%	92.90%	NA
Indica III	913	6.50%	0.20%	1.31%	92.00%	NA
Indica Intermediate	786	13.20%	0.50%	1.27%	84.99%	NA
Temperate Japonica	767	67.00%	18.50%	0.13%	14.34%	NA
Tropical Japonica	504	4.40%	23.40%	0.99%	71.23%	NA
Japonica Intermediate	241	19.10%	7.50%	0.83%	72.61%	NA
VI/Aromatic	96	42.70%	50.00%	0.00%	7.29%	NA
Intermediate	90	21.10%	4.40%	1.11%	73.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1116386156	C -> DEL	LOC_Os11g28470.1	N	frameshift_variant	Average:11.655; most accessible tissue: Callus, score: 52.913	N	N	N	N
vg1116386156	C -> G	LOC_Os11g28470.1	synonymous_variant ; p.Thr322Thr; LOW	synonymous_codon	Average:11.655; most accessible tissue: Callus, score: 52.913	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1116386156	2.76E-06	4.00E-08	mr1836	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
vg1116386156	8.50E-06	NA	mr1946	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
vg1116386156	NA	6.96E-06	mr1994_2	Jap_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