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Detailed information for vg0222121191:

Variant ID: vg0222121191 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 22121191
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, T: 0.00, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:

GATCGGCTATGCTATGAACGTATATAGTCTCATTATTAATATATATTTCGATCTAAGTGATTTATACTGTCTCGGCATAGCGACCGATCTATCCCAATCA[C/T]
TTGATTTAAGTATATATCAATATAAAGATTATATATTGTTAATATCTGCAGTCGATCGAGTAGATTTAGTCCCTTCTTATTTATTAATGGCTGCCGATCG

Reverse complement sequence

CGATCGGCAGCCATTAATAAATAAGAAGGGACTAAATCTACTCGATCGACTGCAGATATTAACAATATATAATCTTTATATTGATATATACTTAAATCAA[G/A]
TGATTGGGATAGATCGGTCGCTATGCCGAGACAGTATAAATCACTTAGATCGAAATATATATTAATAATGAGACTATATACGTTCATAGCATAGCCGATC

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	77.80%	20.60%	0.85%	0.70%	NA
All Indica	2759	71.00%	26.30%	1.45%	1.20%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	27.50%	72.50%	0.00%	0.00%	NA
Indica I	595	89.60%	9.10%	1.34%	0.00%	NA
Indica II	465	75.30%	22.80%	1.51%	0.43%	NA
Indica III	913	56.60%	38.60%	1.75%	3.07%	NA
Indica Intermediate	786	71.20%	27.20%	1.15%	0.38%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	64.60%	35.40%	0.00%	0.00%	NA
Intermediate	90	84.40%	15.60%	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
vg0222121191	C -> T	LOC_Os02g36640.1	upstream_gene_variant ; 366.0bp to feature; MODIFIER	silent_mutation	Average:23.209; most accessible tissue: Zhenshan97 panicle, score: 46.362	N	N	N	N
vg0222121191	C -> T	LOC_Os02g36619.1	downstream_gene_variant ; 3531.0bp to feature; MODIFIER	silent_mutation	Average:23.209; most accessible tissue: Zhenshan97 panicle, score: 46.362	N	N	N	N
vg0222121191	C -> T	LOC_Os02g36619-LOC_Os02g36640	intergenic_region ; MODIFIER	silent_mutation	Average:23.209; most accessible tissue: Zhenshan97 panicle, score: 46.362	N	N	N	N
vg0222121191	C -> DEL	N	N	silent_mutation	Average:23.209; most accessible tissue: Zhenshan97 panicle, score: 46.362	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0222121191	1.52E-06	NA	mr1101	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
vg0222121191	4.88E-06	NA	mr1099_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