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Detailed information for vg1108453091:

Variant ID: vg1108453091 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 8453091
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GATTACAACTTTAGAAGATCGTAACTGGGAAAATGGAAAAAATATACCACCACCCACACACCGACAACACCGACACACAGATCCAGGAGAAGGCTAGCAT[C/T]
GAACCGGCCACCGCTAAGCGTGGCCGACCGCCGTAGGTCAACAAAGGAACACAAACAAGAACGCCCAATAAACGCCCTTACAACCAACACAAAGCCCAAC

Reverse complement sequence

GTTGGGCTTTGTGTTGGTTGTAAGGGCGTTTATTGGGCGTTCTTGTTTGTGTTCCTTTGTTGACCTACGGCGGTCGGCCACGCTTAGCGGTGGCCGGTTC[G/A]
ATGCTAGCCTTCTCCTGGATCTGTGTGTCGGTGTTGTCGGTGTGTGGGTGGTGGTATATTTTTTCCATTTTCCCAGTTACGATCTTCTAAAGTTGTAATC

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	99.30%	0.30%	0.44%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	97.70%	0.90%	1.39%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	96.20%	1.70%	2.09%	0.00%	NA
Tropical Japonica	504	99.40%	0.00%	0.60%	0.00%	NA
Japonica Intermediate	241	98.80%	0.40%	0.83%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1108453091	C -> T	LOC_Os11g15010.1	upstream_gene_variant ; 3511.0bp to feature; MODIFIER	silent_mutation	Average:70.069; most accessible tissue: Zhenshan97 young leaf, score: 84.431	N	N	N	N
vg1108453091	C -> T	LOC_Os11g15030.1	upstream_gene_variant ; 4044.0bp to feature; MODIFIER	silent_mutation	Average:70.069; most accessible tissue: Zhenshan97 young leaf, score: 84.431	N	N	N	N
vg1108453091	C -> T	LOC_Os11g15020.1	downstream_gene_variant ; 735.0bp to feature; MODIFIER	silent_mutation	Average:70.069; most accessible tissue: Zhenshan97 young leaf, score: 84.431	N	N	N	N
vg1108453091	C -> T	LOC_Os11g15010-LOC_Os11g15020	intergenic_region ; MODIFIER	silent_mutation	Average:70.069; most accessible tissue: Zhenshan97 young leaf, score: 84.431	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1108453091	NA	1.80E-06	mr1280	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
vg1108453091	3.87E-06	1.14E-07	mr1563_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