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Detailed information for vg0116559161:

Variant ID: vg0116559161 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 16559161
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:

GCTCGGCTTGGGACTTGAGGCAAACGGAAGAGGACGACAAGGGGATGCTTTATATAGGCTTGGACTAGAGAGATCGGACTCCAAATGAGAGGATTTGAGC[T/C]
GGAAAATCCGAGGGTTAGTTTGGAGAGATAAACTCGAAAACGAATTCGATTCGGTTTATCCGGGCAAAATTAATCTCCGAGACTTTAGGGGAAAGGAAGA

Reverse complement sequence

TCTTCCTTTCCCCTAAAGTCTCGGAGATTAATTTTGCCCGGATAAACCGAATCGAATTCGTTTTCGAGTTTATCTCTCCAAACTAACCCTCGGATTTTCC[A/G]
GCTCAAATCCTCTCATTTGGAGTCCGATCTCTCTAGTCCAAGCCTATATAAAGCATCCCCTTGTCGTCCTCTTCCGTTTGCCTCAAGTCCCAAGCCGAGC

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	62.60%	37.20%	0.19%	0.00%	NA
All Indica	2759	96.80%	3.00%	0.22%	0.00%	NA
All Japonica	1512	4.00%	96.00%	0.00%	0.00%	NA
Aus	269	67.70%	32.00%	0.37%	0.00%	NA
Indica I	595	97.10%	2.40%	0.50%	0.00%	NA
Indica II	465	95.50%	4.50%	0.00%	0.00%	NA
Indica III	913	99.10%	0.80%	0.11%	0.00%	NA
Indica Intermediate	786	94.50%	5.20%	0.25%	0.00%	NA
Temperate Japonica	767	1.20%	98.80%	0.00%	0.00%	NA
Tropical Japonica	504	5.60%	94.40%	0.00%	0.00%	NA
Japonica Intermediate	241	10.00%	90.00%	0.00%	0.00%	NA
VI/Aromatic	96	6.20%	93.80%	0.00%	0.00%	NA
Intermediate	90	44.40%	53.30%	2.22%	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
vg0116559161	T -> C	LOC_Os01g29530.1	upstream_gene_variant ; 1349.0bp to feature; MODIFIER	silent_mutation	Average:65.711; most accessible tissue: Zhenshan97 panicle, score: 92.403	N	N	N	N
vg0116559161	T -> C	LOC_Os01g29550.1	upstream_gene_variant ; 3608.0bp to feature; MODIFIER	silent_mutation	Average:65.711; most accessible tissue: Zhenshan97 panicle, score: 92.403	N	N	N	N
vg0116559161	T -> C	LOC_Os01g29540.1	downstream_gene_variant ; 567.0bp to feature; MODIFIER	silent_mutation	Average:65.711; most accessible tissue: Zhenshan97 panicle, score: 92.403	N	N	N	N
vg0116559161	T -> C	LOC_Os01g29530-LOC_Os01g29540	intergenic_region ; MODIFIER	silent_mutation	Average:65.711; most accessible tissue: Zhenshan97 panicle, score: 92.403	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0116559161	1.13E-06	1.13E-06	mr1499	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
vg0116559161	NA	2.70E-51	mr1519	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
vg0116559161	NA	1.28E-07	mr1335_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
vg0116559161	2.55E-06	7.06E-53	mr1519_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
vg0116559161	NA	4.79E-13	mr1770_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