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Detailed information for vg1109858246:

Variant ID: vg1109858246 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 9858246
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGGAATTCCCTCCTAATTACCACCTACTACCCAGGTACTAAAAAGAGGGAGTTTCTTCCTCAATTCCCCATCCCCATTCCACCAAAATTCTCATGTATCC[C/T]
AACCAAACAAAGCAGTTAATAGCCTCATCTCTCTAAACTCCCAATCCCTCCTTAAAAACTCCCTCCAACCAAACAGGCCGTAAAGTATTTTTCGTTTAAT

Reverse complement sequence

ATTAAACGAAAAATACTTTACGGCCTGTTTGGTTGGAGGGAGTTTTTAAGGAGGGATTGGGAGTTTAGAGAGATGAGGCTATTAACTGCTTTGTTTGGTT[G/A]
GGATACATGAGAATTTTGGTGGAATGGGGATGGGGAATTGAGGAAGAAACTCCCTCTTTTTAGTACCTGGGTAGTAGGTGGTAATTAGGAGGGAATTCCT

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	41.20%	3.90%	0.36%	54.55%	NA
All Indica	2759	14.50%	6.10%	0.40%	79.09%	NA
All Japonica	1512	95.60%	0.80%	0.13%	3.44%	NA
Aus	269	14.90%	0.70%	0.74%	83.64%	NA
Indica I	595	20.30%	5.90%	0.50%	73.28%	NA
Indica II	465	10.80%	0.90%	1.08%	87.31%	NA
Indica III	913	5.70%	10.10%	0.11%	84.12%	NA
Indica Intermediate	786	22.40%	4.60%	0.25%	72.77%	NA
Temperate Japonica	767	96.60%	0.00%	0.26%	3.13%	NA
Tropical Japonica	504	94.20%	2.40%	0.00%	3.37%	NA
Japonica Intermediate	241	95.40%	0.00%	0.00%	4.56%	NA
VI/Aromatic	96	21.90%	0.00%	1.04%	77.08%	NA
Intermediate	90	44.40%	4.40%	1.11%	50.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1109858246	C -> T	LOC_Os11g17660.1	upstream_gene_variant ; 840.0bp to feature; MODIFIER	silent_mutation	Average:15.479; most accessible tissue: Callus, score: 57.262	N	N	N	N
vg1109858246	C -> T	LOC_Os11g17670.1	upstream_gene_variant ; 3764.0bp to feature; MODIFIER	silent_mutation	Average:15.479; most accessible tissue: Callus, score: 57.262	N	N	N	N
vg1109858246	C -> T	LOC_Os11g17660-LOC_Os11g17670	intergenic_region ; MODIFIER	silent_mutation	Average:15.479; most accessible tissue: Callus, score: 57.262	N	N	N	N
vg1109858246	C -> DEL	N	N	silent_mutation	Average:15.479; most accessible tissue: Callus, score: 57.262	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1109858246	4.15E-06	NA	mr1155_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