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Detailed information for vg1122622039:

Variant ID: vg1122622039 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 22622039
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, T: 0.07, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

ATGATAGCAATTCCAATTCCTTCCTAATACGATCCTCATCCATAAGCCTCATGAGATACTGCAGGTATCAAGAGAAAACCAGAGAGGTAAAATAATTTGC[C/T]
GGGCCGGCCAAAGAGAAGTAAAATAATAGCTAAATATCAAAAACTGAAGGAGCCAAAGACAAGTTACCTGAAGAATGACAGCCAAAGGAACCTCTGGTTC

Reverse complement sequence

GAACCAGAGGTTCCTTTGGCTGTCATTCTTCAGGTAACTTGTCTTTGGCTCCTTCAGTTTTTGATATTTAGCTATTATTTTACTTCTCTTTGGCCGGCCC[G/A]
GCAAATTATTTTACCTCTCTGGTTTTCTCTTGATACCTGCAGTATCTCATGAGGCTTATGGATGAGGATCGTATTAGGAAGGAATTGGAATTGCTATCAT

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	57.90%	17.40%	0.89%	23.87%	NA
All Indica	2759	43.00%	28.90%	0.69%	27.36%	NA
All Japonica	1512	88.40%	1.10%	0.33%	10.12%	NA
Aus	269	23.80%	0.00%	5.95%	70.26%	NA
Indica I	595	11.60%	71.40%	0.50%	16.47%	NA
Indica II	465	90.10%	3.40%	0.00%	6.45%	NA
Indica III	913	28.50%	20.30%	1.42%	49.84%	NA
Indica Intermediate	786	55.90%	21.90%	0.38%	21.88%	NA
Temperate Japonica	767	94.50%	2.00%	0.00%	3.52%	NA
Tropical Japonica	504	82.10%	0.20%	0.40%	17.26%	NA
Japonica Intermediate	241	82.20%	0.40%	1.24%	16.18%	NA
VI/Aromatic	96	85.40%	0.00%	0.00%	14.58%	NA
Intermediate	90	72.20%	6.70%	2.22%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1122622039	C -> T	LOC_Os11g38160.1	upstream_gene_variant ; 3491.0bp to feature; MODIFIER	silent_mutation	Average:29.134; most accessible tissue: Callus, score: 75.039	N	N	N	N
vg1122622039	C -> T	LOC_Os11g38150.1	intron_variant ; MODIFIER	silent_mutation	Average:29.134; most accessible tissue: Callus, score: 75.039	N	N	N	N
vg1122622039	C -> DEL	N	N	silent_mutation	Average:29.134; most accessible tissue: Callus, score: 75.039	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1122622039	NA	1.01E-06	mr1942	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
vg1122622039	NA	4.20E-06	mr1036_2	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
vg1122622039	NA	1.93E-06	mr1169_2	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
vg1122622039	NA	4.97E-08	mr1923_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
vg1122622039	NA	2.00E-08	mr1923_2	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
vg1122622039	NA	3.37E-08	mr1933_2	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