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Detailed information for vg1102224382:

Variant ID: vg1102224382 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 2224382
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.61, C: 0.38, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

TAGAAAAAACAAATGAATAACCGTTTGGTTGGACCGAAAGAAATACATATGAATTTGAAGAGGGATAAAGACTTAAAGAAAACTTTCTCAGGTTCTACAT[T/C]
ATGTTAAATTTTCTATAAAACTTGCATGGAATGAAATATTACATAGGAATTACATAGGACTATATGATTCATTCCTTTAACTTTAAGGGCTATATAGAAA

Reverse complement sequence

TTTCTATATAGCCCTTAAAGTTAAAGGAATGAATCATATAGTCCTATGTAATTCCTATGTAATATTTCATTCCATGCAAGTTTTATAGAAAATTTAACAT[A/G]
ATGTAGAACCTGAGAAAGTTTTCTTTAAGTCTTTATCCCTCTTCAAATTCATATGTATTTCTTTCGGTCCAACCAAACGGTTATTCATTTGTTTTTTCTA

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	60.90%	38.90%	0.17%	0.00%	NA
All Indica	2759	91.30%	8.50%	0.14%	0.00%	NA
All Japonica	1512	2.60%	97.30%	0.07%	0.00%	NA
Aus	269	82.20%	17.80%	0.00%	0.00%	NA
Indica I	595	97.30%	2.70%	0.00%	0.00%	NA
Indica II	465	96.80%	3.20%	0.00%	0.00%	NA
Indica III	913	87.30%	12.50%	0.22%	0.00%	NA
Indica Intermediate	786	88.30%	11.50%	0.25%	0.00%	NA
Temperate Japonica	767	2.50%	97.40%	0.13%	0.00%	NA
Tropical Japonica	504	1.60%	98.40%	0.00%	0.00%	NA
Japonica Intermediate	241	5.40%	94.60%	0.00%	0.00%	NA
VI/Aromatic	96	59.40%	38.50%	2.08%	0.00%	NA
Intermediate	90	45.60%	53.30%	1.11%	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
vg1102224382	T -> C	LOC_Os11g05070.1	upstream_gene_variant ; 3634.0bp to feature; MODIFIER	silent_mutation	Average:55.838; most accessible tissue: Zhenshan97 flower, score: 84.409	N	N	N	N
vg1102224382	T -> C	LOC_Os11g05080.1	upstream_gene_variant ; 366.0bp to feature; MODIFIER	silent_mutation	Average:55.838; most accessible tissue: Zhenshan97 flower, score: 84.409	N	N	N	N
vg1102224382	T -> C	LOC_Os11g05070-LOC_Os11g05080	intergenic_region ; MODIFIER	silent_mutation	Average:55.838; most accessible tissue: Zhenshan97 flower, score: 84.409	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1102224382	NA	2.48E-06	mr1168	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
vg1102224382	8.65E-07	2.53E-06	mr1310	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
vg1102224382	NA	7.61E-12	mr1751	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
vg1102224382	NA	1.33E-10	mr1904	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