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Detailed information for vg1119299829:

Variant ID: vg1119299829 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 19299829
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: 103. )

Flanking Sequence (100 bp) in Reference Genome:

TGCCTCTATTGCATTTCACGTTCACGTTCATTCACGTTCACATTCGTTAACGTTCGTTCACGTTCGTTAGTTCATGTTCACGTTCATTGACGTTCGTTCA[C/T]
GCTCGTTCGTTCACGTTCGTTCGCTCGTTCACTTTCTCGTTCACGTTCGTTCGCTTGTTCTCGTTCACATTCGTTCGCTCGTTCATGTTAGTTCACGTTA

Reverse complement sequence

TAACGTGAACTAACATGAACGAGCGAACGAATGTGAACGAGAACAAGCGAACGAACGTGAACGAGAAAGTGAACGAGCGAACGAACGTGAACGAACGAGC[G/A]
TGAACGAACGTCAATGAACGTGAACATGAACTAACGAACGTGAACGAACGTTAACGAATGTGAACGTGAATGAACGTGAACGTGAAATGCAATAGAGGCA

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	97.20%	2.10%	0.23%	0.49%	NA
All Indica	2759	96.30%	3.50%	0.25%	0.00%	NA
All Japonica	1512	98.30%	0.10%	0.26%	1.39%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.50%	1.30%	0.17%	0.00%	NA
Indica II	465	91.80%	7.50%	0.65%	0.00%	NA
Indica III	913	98.70%	1.20%	0.11%	0.00%	NA
Indica Intermediate	786	94.40%	5.30%	0.25%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	95.00%	0.00%	0.79%	4.17%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	0.00%	0.00%	2.08%	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
vg1119299829	C -> T	LOC_Os11g32680.1	upstream_gene_variant ; 932.0bp to feature; MODIFIER	silent_mutation	Average:25.557; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg1119299829	C -> T	LOC_Os11g32690.1	downstream_gene_variant ; 1604.0bp to feature; MODIFIER	silent_mutation	Average:25.557; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg1119299829	C -> T	LOC_Os11g32680-LOC_Os11g32690	intergenic_region ; MODIFIER	silent_mutation	Average:25.557; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg1119299829	C -> DEL	N	N	silent_mutation	Average:25.557; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1119299829	NA	4.97E-07	mr1082	Ind_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
vg1119299829	NA	3.69E-06	mr1354	Ind_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
vg1119299829	NA	1.38E-08	mr1354_2	Ind_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
vg1119299829	NA	3.21E-06	mr1402_2	Ind_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
vg1119299829	NA	2.81E-08	mr1408_2	Ind_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