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Detailed information for vg1121280481:

Variant ID: vg1121280481 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21280481
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.06, others allele: 0.00, population size: 159. )

Flanking Sequence (100 bp) in Reference Genome:

ATGTGAACGACAAAAACAATTGCACAGTTTGCATATAAATCGCGAGACGAATTTTTAAGCCTAATTACGCTATAATTTGACAATGTGTTCCTACAGTAAA[T/C]
ATTTGCTAATGACAGATTAGTTAGGCTTAATAGATTCGTCTTGCAGTTCACCTGTGGAATCTATAATTTGTTTTGTTATTAATCTATATTTAATACTTCA

Reverse complement sequence

TGAAGTATTAAATATAGATTAATAACAAAACAAATTATAGATTCCACAGGTGAACTGCAAGACGAATCTATTAAGCCTAACTAATCTGTCATTAGCAAAT[A/G]
TTTACTGTAGGAACACATTGTCAAATTATAGCGTAATTAGGCTTAAAAATTCGTCTCGCGATTTATATGCAAACTGTGCAATTGTTTTTGTCGTTCACAT

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	36.40%	35.60%	1.86%	26.13%	NA
All Indica	2759	18.00%	42.00%	2.94%	37.01%	NA
All Japonica	1512	76.50%	17.10%	0.20%	6.28%	NA
Aus	269	11.90%	52.00%	0.00%	36.06%	NA
Indica I	595	22.50%	36.30%	2.35%	38.82%	NA
Indica II	465	3.20%	56.80%	3.01%	36.99%	NA
Indica III	913	27.70%	32.40%	2.63%	37.24%	NA
Indica Intermediate	786	12.10%	48.90%	3.69%	35.37%	NA
Temperate Japonica	767	86.70%	12.00%	0.26%	1.04%	NA
Tropical Japonica	504	61.50%	23.60%	0.20%	14.68%	NA
Japonica Intermediate	241	75.10%	19.50%	0.00%	5.39%	NA
VI/Aromatic	96	4.20%	90.60%	0.00%	5.21%	NA
Intermediate	90	33.30%	43.30%	4.44%	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
vg1121280481	T -> DEL	N	N	silent_mutation	Average:32.012; most accessible tissue: Callus, score: 55.735	N	N	N	N
vg1121280481	T -> C	LOC_Os11g36180.1	upstream_gene_variant ; 3038.0bp to feature; MODIFIER	silent_mutation	Average:32.012; most accessible tissue: Callus, score: 55.735	N	N	N	N
vg1121280481	T -> C	LOC_Os11g36190.1	downstream_gene_variant ; 4374.0bp to feature; MODIFIER	silent_mutation	Average:32.012; most accessible tissue: Callus, score: 55.735	N	N	N	N
vg1121280481	T -> C	LOC_Os11g36190.2	downstream_gene_variant ; 4374.0bp to feature; MODIFIER	silent_mutation	Average:32.012; most accessible tissue: Callus, score: 55.735	N	N	N	N
vg1121280481	T -> C	LOC_Os11g36180-LOC_Os11g36190	intergenic_region ; MODIFIER	silent_mutation	Average:32.012; most accessible tissue: Callus, score: 55.735	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121280481	NA	8.06E-07	mr1709	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
vg1121280481	NA	2.11E-07	mr1517_2	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
vg1121280481	3.85E-06	3.85E-06	mr1541_2	Jap_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