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Detailed information for vg1110837955:

Variant ID: vg1110837955 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 10837955
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.83, T: 0.16, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:

AGCTTTGCACTTTATTTAGAATATTCATCTTTATACATTTCTGGTATTGAAATACTTTCCGAGTATATGAATGCCAACTTTACTTTATGTTCATATTATA[C/T]
TGATTATACTGCTAGCTTATCTGGGAGATGCATAGGTATGTGTATAATGTTTGCTTATGCAGTTACTCTATGCCATGACGATGATATTAGAGTAGTATCT

Reverse complement sequence

AGATACTACTCTAATATCATCGTCATGGCATAGAGTAACTGCATAAGCAAACATTATACACATACCTATGCATCTCCCAGATAAGCTAGCAGTATAATCA[G/A]
TATAATATGAACATAAAGTAAAGTTGGCATTCATATACTCGGAAAGTATTTCAATACCAGAAATGTATAAAGATGAATATTCTAAATAAAGTGCAAAGCT

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	62.20%	37.70%	0.13%	0.00%	NA
All Indica	2759	93.10%	6.80%	0.07%	0.00%	NA
All Japonica	1512	2.70%	97.20%	0.07%	0.00%	NA
Aus	269	98.90%	1.10%	0.00%	0.00%	NA
Indica I	595	94.80%	5.00%	0.17%	0.00%	NA
Indica II	465	98.70%	1.30%	0.00%	0.00%	NA
Indica III	913	98.10%	1.90%	0.00%	0.00%	NA
Indica Intermediate	786	82.70%	17.20%	0.13%	0.00%	NA
Temperate Japonica	767	3.30%	96.60%	0.13%	0.00%	NA
Tropical Japonica	504	2.80%	97.20%	0.00%	0.00%	NA
Japonica Intermediate	241	0.80%	99.20%	0.00%	0.00%	NA
VI/Aromatic	96	11.50%	88.50%	0.00%	0.00%	NA
Intermediate	90	58.90%	37.80%	3.33%	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
vg1110837955	C -> T	LOC_Os11g19010.1	upstream_gene_variant ; 785.0bp to feature; MODIFIER	silent_mutation	Average:35.738; most accessible tissue: Zhenshan97 flag leaf, score: 50.663	N	N	N	N
vg1110837955	C -> T	LOC_Os11g19020.1	upstream_gene_variant ; 2085.0bp to feature; MODIFIER	silent_mutation	Average:35.738; most accessible tissue: Zhenshan97 flag leaf, score: 50.663	N	N	N	N
vg1110837955	C -> T	LOC_Os11g19000.1	downstream_gene_variant ; 714.0bp to feature; MODIFIER	silent_mutation	Average:35.738; most accessible tissue: Zhenshan97 flag leaf, score: 50.663	N	N	N	N
vg1110837955	C -> T	LOC_Os11g19000-LOC_Os11g19010	intergenic_region ; MODIFIER	silent_mutation	Average:35.738; most accessible tissue: Zhenshan97 flag leaf, score: 50.663	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1110837955	NA	4.66E-06	mr1217	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
vg1110837955	NA	5.24E-10	mr1595	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