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Detailed information for vg1121036873:

Variant ID: vg1121036873 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21036873
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTTGCTTATTTCCACCAAGCCGACAACTTATACGACAAAGCGTATGTTTTTGCACTTGTTACTTGGGCCAGGTTAATTAGACAGGCAACTGCAAATTAAG[C/T]
ACTTCAAATCATATGCTTGTTCTGCTTCCTACAACTGACAGGTTTACTGGTATGAATGAATAAATGAAGGTGGAGAGGCACTCAAAAGAAAATGTCATTC

Reverse complement sequence

GAATGACATTTTCTTTTGAGTGCCTCTCCACCTTCATTTATTCATTCATACCAGTAAACCTGTCAGTTGTAGGAAGCAGAACAAGCATATGATTTGAAGT[G/A]
CTTAATTTGCAGTTGCCTGTCTAATTAACCTGGCCCAAGTAACAAGTGCAAAAACATACGCTTTGTCGTATAAGTTGTCGGCTTGGTGGAAATAAGCAAC

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	69.10%	10.30%	0.63%	19.97%	NA
All Indica	2759	51.80%	15.00%	0.87%	32.37%	NA
All Japonica	1512	95.40%	2.60%	0.07%	1.92%	NA
Aus	269	93.30%	1.90%	1.49%	3.35%	NA
Indica I	595	79.30%	9.60%	0.50%	10.59%	NA
Indica II	465	47.10%	25.80%	1.08%	26.02%	NA
Indica III	913	42.90%	7.60%	0.88%	48.63%	NA
Indica Intermediate	786	44.00%	21.20%	1.02%	33.72%	NA
Temperate Japonica	767	95.40%	4.20%	0.00%	0.39%	NA
Tropical Japonica	504	94.00%	0.60%	0.20%	5.16%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	85.40%	11.50%	0.00%	3.12%	NA
Intermediate	90	67.80%	20.00%	1.11%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121036873	C -> T	LOC_Os11g35850.1	upstream_gene_variant ; 3990.0bp to feature; MODIFIER	silent_mutation	Average:32.47; most accessible tissue: Callus, score: 54.533	N	N	N	N
vg1121036873	C -> T	LOC_Os11g35840.1	downstream_gene_variant ; 119.0bp to feature; MODIFIER	silent_mutation	Average:32.47; most accessible tissue: Callus, score: 54.533	N	N	N	N
vg1121036873	C -> T	LOC_Os11g35840-LOC_Os11g35850	intergenic_region ; MODIFIER	silent_mutation	Average:32.47; most accessible tissue: Callus, score: 54.533	N	N	N	N
vg1121036873	C -> DEL	N	N	silent_mutation	Average:32.47; most accessible tissue: Callus, score: 54.533	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121036873	3.72E-06	NA	mr1446	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
vg1121036873	8.75E-06	NA	mr1655	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