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Detailed information for vg1116397469:

Variant ID: vg1116397469 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 16397469
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.04, others allele: 0.00, population size: 51. )

Flanking Sequence (100 bp) in Reference Genome:

TTAGGTTCACTAAAGAACGGATCATAGCCATATACTACTAGGCAAAATTTGTTGCAGGACATCTAAACAACGTGCAAGAACACGTTTATGCTATAGGGCA[C/T]
TATAAAAAAGTGGTAATTAGTTGCTCGATACACACAACATTATTTTATTATATCCGGAGGAATTGGAAAGTGAAACCGCTGCGAAAGTATGTTTTTACCC

Reverse complement sequence

GGGTAAAAACATACTTTCGCAGCGGTTTCACTTTCCAATTCCTCCGGATATAATAAAATAATGTTGTGTGTATCGAGCAACTAATTACCACTTTTTTATA[G/A]
TGCCCTATAGCATAAACGTGTTCTTGCACGTTGTTTAGATGTCCTGCAACAAATTTTGCCTAGTAGTATATGGCTATGATCCGTTCTTTAGTGAACCTAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	65.00%	20.00%	0.42%	14.64%	NA
All Indica	2759	78.10%	5.90%	0.62%	15.37%	NA
All Japonica	1512	43.60%	47.00%	0.13%	9.26%	NA
Aus	269	68.80%	2.60%	0.00%	28.62%	NA
Indica I	595	75.80%	7.90%	0.50%	15.80%	NA
Indica II	465	91.80%	3.40%	0.00%	4.73%	NA
Indica III	913	72.40%	5.90%	0.33%	21.36%	NA
Indica Intermediate	786	78.50%	5.70%	1.40%	14.38%	NA
Temperate Japonica	767	15.10%	68.20%	0.13%	16.56%	NA
Tropical Japonica	504	72.20%	26.40%	0.20%	1.19%	NA
Japonica Intermediate	241	74.30%	22.80%	0.00%	2.90%	NA
VI/Aromatic	96	11.50%	50.00%	1.04%	37.50%	NA
Intermediate	90	66.70%	16.70%	0.00%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1116397469	C -> T	LOC_Os11g28480.1	upstream_gene_variant ; 2274.0bp to feature; MODIFIER	silent_mutation	Average:45.246; most accessible tissue: Callus, score: 87.071	N	N	N	N
vg1116397469	C -> T	LOC_Os11g28480-LOC_Os11g28490	intergenic_region ; MODIFIER	silent_mutation	Average:45.246; most accessible tissue: Callus, score: 87.071	N	N	N	N
vg1116397469	C -> DEL	N	N	silent_mutation	Average:45.246; most accessible tissue: Callus, score: 87.071	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1116397469	NA	8.92E-08	mr1229	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
vg1116397469	1.27E-06	7.30E-07	mr1530	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
vg1116397469	NA	1.46E-08	mr1530	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
vg1116397469	NA	9.36E-09	mr1629	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
vg1116397469	NA	1.50E-06	mr1982	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