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Detailed information for vg1120458011:

Variant ID: vg1120458011 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 20458011
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTATGAAAAAAATATAAAGATATTAGCCGCGCAATATACGCCAGCCACCATGCTATTCAGTAAGGGGGTGTTTATTAAGCCTAATTAATCCATCATTAG[C/T]
AAATGTTTACTGTAGCACCATATTATCAAAATCATGGAGTAATTAGGTGTTGGGGAAGAAGAGGCACAAAGAGTGGCTGATCTGTTTAATTGTAAGAGAG

Reverse complement sequence

CTCTCTTACAATTAAACAGATCAGCCACTCTTTGTGCCTCTTCTTCCCCAACACCTAATTACTCCATGATTTTGATAATATGGTGCTACAGTAAACATTT[G/A]
CTAATGATGGATTAATTAGGCTTAATAAACACCCCCTTACTGAATAGCATGGTGGCTGGCGTATATTGCGCGGCTAATATCTTTATATTTTTTTCATAAT

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	49.90%	26.60%	1.88%	21.69%	NA
All Indica	2759	65.00%	3.20%	2.61%	29.25%	NA
All Japonica	1512	33.80%	60.80%	0.07%	5.36%	NA
Aus	269	1.90%	49.10%	4.46%	44.61%	NA
Indica I	595	50.10%	1.20%	0.34%	48.40%	NA
Indica II	465	76.80%	1.10%	1.08%	21.08%	NA
Indica III	913	63.60%	3.40%	6.35%	26.62%	NA
Indica Intermediate	786	70.90%	5.60%	0.89%	22.65%	NA
Temperate Japonica	767	16.30%	79.50%	0.13%	4.04%	NA
Tropical Japonica	504	45.20%	45.20%	0.00%	9.52%	NA
Japonica Intermediate	241	65.60%	33.60%	0.00%	0.83%	NA
VI/Aromatic	96	4.20%	83.30%	3.12%	9.38%	NA
Intermediate	90	48.90%	41.10%	1.11%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1120458011	C -> T	LOC_Os11g34910.1	3_prime_UTR_variant ; 1336.0bp to feature; MODIFIER	silent_mutation	Average:34.948; most accessible tissue: Callus, score: 82.87	N	N	N	N
vg1120458011	C -> T	LOC_Os11g34900.1	upstream_gene_variant ; 3243.0bp to feature; MODIFIER	silent_mutation	Average:34.948; most accessible tissue: Callus, score: 82.87	N	N	N	N
vg1120458011	C -> T	LOC_Os11g34920.1	upstream_gene_variant ; 3099.0bp to feature; MODIFIER	silent_mutation	Average:34.948; most accessible tissue: Callus, score: 82.87	N	N	N	N
vg1120458011	C -> T	LOC_Os11g34890.1	downstream_gene_variant ; 4439.0bp to feature; MODIFIER	silent_mutation	Average:34.948; most accessible tissue: Callus, score: 82.87	N	N	N	N
vg1120458011	C -> DEL	N	N	silent_mutation	Average:34.948; most accessible tissue: Callus, score: 82.87	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1120458011	2.96E-06	NA	mr1739	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