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Detailed information for vg1121178330:

Variant ID: vg1121178330 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21178330
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:

TCCTGAGAGCAAGTTTAATATAGCCAATTACTAGCTCCAATTCATATATAGCCAATCTAATAGCTCATTCATACAATAGTTACATACTACACTATCAATA[C/T]
CTGGTCCCACCTATCATACACACACTGTGTCTTGGAGTCCGTGCTACAACTGGCTACAAATCTGTAGCCCGCTGCCCTTCTCTCTCCTCATTTATCTACT

Reverse complement sequence

AGTAGATAAATGAGGAGAGAGAAGGGCAGCGGGCTACAGATTTGTAGCCAGTTGTAGCACGGACTCCAAGACACAGTGTGTGTATGATAGGTGGGACCAG[G/A]
TATTGATAGTGTAGTATGTAACTATTGTATGAATGAGCTATTAGATTGGCTATATATGAATTGGAGCTAGTAATTGGCTATATTAAACTTGCTCTCAGGA

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	55.40%	3.80%	13.86%	26.94%	NA
All Indica	2759	41.90%	1.20%	15.62%	41.25%	NA
All Japonica	1512	72.80%	9.50%	11.57%	6.08%	NA
Aus	269	75.10%	0.40%	14.87%	9.67%	NA
Indica I	595	27.10%	1.20%	38.99%	32.77%	NA
Indica II	465	33.50%	2.20%	17.63%	46.67%	NA
Indica III	913	51.60%	0.80%	2.85%	44.80%	NA
Indica Intermediate	786	46.80%	1.30%	11.58%	40.33%	NA
Temperate Japonica	767	62.10%	14.70%	20.08%	3.13%	NA
Tropical Japonica	504	84.50%	1.00%	2.78%	11.71%	NA
Japonica Intermediate	241	82.60%	10.80%	2.90%	3.73%	NA
VI/Aromatic	96	96.90%	0.00%	1.04%	2.08%	NA
Intermediate	90	73.30%	1.10%	8.89%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121178330	C -> T	LOC_Os11g36030.1	3_prime_UTR_variant ; 495.0bp to feature; MODIFIER	silent_mutation	Average:55.947; most accessible tissue: Minghui63 panicle, score: 83.421	N	N	N	N
vg1121178330	C -> T	LOC_Os11g36020.1	downstream_gene_variant ; 675.0bp to feature; MODIFIER	silent_mutation	Average:55.947; most accessible tissue: Minghui63 panicle, score: 83.421	N	N	N	N
vg1121178330	C -> DEL	N	N	silent_mutation	Average:55.947; most accessible tissue: Minghui63 panicle, score: 83.421	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121178330	NA	2.07E-08	mr1770	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
vg1121178330	2.84E-06	NA	mr1183_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