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Detailed information for vg1108531956:

Variant ID: vg1108531956 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 8531956
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: 268. )

Flanking Sequence (100 bp) in Reference Genome:

GTTTCCGACAGAGTTAGCTACAATATGTCAGAATCTAAAGGATATATTTGTAATGGGAGGGGATTTTAATATTACTAGATGGGCACCCTACGTGTTATTG[C/T]
GGGAGAATTGTGTGATAATATAGTATATATGAGTTCTAAAATTTTCTTTCTTACCTACTATACGATTTTTTTATATGTTTATATATTTTTGTACATTTAT

Reverse complement sequence

ATAAATGTACAAAAATATATAAACATATAAAAAAATCGTATAGTAGGTAAGAAAGAAAATTTTAGAACTCATATATACTATATTATCACACAATTCTCCC[G/A]
CAATAACACGTAGGGTGCCCATCTAGTAATATTAAAATCCCCTCCCATTACAAATATATCCTTTAGATTCTGACATATTGTAGCTAACTCTGTCGGAAAC

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	88.80%	9.10%	2.07%	0.00%	NA
All Indica	2759	99.30%	0.50%	0.25%	0.00%	NA
All Japonica	1512	69.70%	24.80%	5.49%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.20%	0.00%	0.84%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.70%	0.30%	0.00%	0.00%	NA
Indica Intermediate	786	98.50%	1.30%	0.25%	0.00%	NA
Temperate Japonica	767	82.80%	10.70%	6.52%	0.00%	NA
Tropical Japonica	504	46.60%	49.40%	3.97%	0.00%	NA
Japonica Intermediate	241	76.30%	18.30%	5.39%	0.00%	NA
VI/Aromatic	96	61.50%	34.40%	4.17%	0.00%	NA
Intermediate	90	85.60%	10.00%	4.44%	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
vg1108531956	C -> T	LOC_Os11g15140.1	upstream_gene_variant ; 3108.0bp to feature; MODIFIER	silent_mutation	Average:45.074; most accessible tissue: Zhenshan97 young leaf, score: 64.205	N	N	N	N
vg1108531956	C -> T	LOC_Os11g15130.1	downstream_gene_variant ; 613.0bp to feature; MODIFIER	silent_mutation	Average:45.074; most accessible tissue: Zhenshan97 young leaf, score: 64.205	N	N	N	N
vg1108531956	C -> T	LOC_Os11g15130-LOC_Os11g15140	intergenic_region ; MODIFIER	silent_mutation	Average:45.074; most accessible tissue: Zhenshan97 young leaf, score: 64.205	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1108531956	NA	1.54E-06	mr1188	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
vg1108531956	NA	6.75E-06	mr1418	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
vg1108531956	NA	5.35E-06	mr1906	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
vg1108531956	2.62E-06	NA	mr1733_2	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