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Detailed information for vg1116562086:

Variant ID: vg1116562086 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 16562086
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAAATTATATGCCTACATAAAAATATATTTAACAATAAATCAAATGATAGGAAAAGAATTAATAATTACTTAAATTTTTTGAATAAGACGAACGGTCAAA[T/C]
ATATGCTAAAAAGTCAACGACGTCAAATATTTTAAAACGGAGGGAGTAATAACAAGAAGAGCAAGTTTCATAGCTTATACAACTTTGCTTGTATGCTAGG

Reverse complement sequence

CCTAGCATACAAGCAAAGTTGTATAAGCTATGAAACTTGCTCTTCTTGTTATTACTCCCTCCGTTTTAAAATATTTGACGTCGTTGACTTTTTAGCATAT[A/G]
TTTGACCGTTCGTCTTATTCAAAAAATTTAAGTAATTATTAATTCTTTTCCTATCATTTGATTTATTGTTAAATATATTTTTATGTAGGCATATAATTTG

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	50.10%	35.30%	1.99%	12.59%	NA
All Indica	2759	75.20%	3.60%	2.14%	19.06%	NA
All Japonica	1512	1.90%	93.90%	0.00%	4.17%	NA
Aus	269	76.60%	11.90%	11.52%	0.00%	NA
Indica I	595	85.50%	2.20%	3.19%	9.08%	NA
Indica II	465	89.50%	0.90%	2.37%	7.31%	NA
Indica III	913	61.60%	3.60%	1.10%	33.73%	NA
Indica Intermediate	786	74.90%	6.10%	2.42%	16.54%	NA
Temperate Japonica	767	2.10%	96.60%	0.00%	1.30%	NA
Tropical Japonica	504	2.00%	88.70%	0.00%	9.33%	NA
Japonica Intermediate	241	1.20%	96.30%	0.00%	2.49%	NA
VI/Aromatic	96	9.40%	90.60%	0.00%	0.00%	NA
Intermediate	90	53.30%	35.60%	4.44%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1116562086	T -> DEL	N	N	silent_mutation	Average:21.697; most accessible tissue: Zhenshan97 young leaf, score: 43.23	N	N	N	N
vg1116562086	T -> C	LOC_Os11g28640.1	upstream_gene_variant ; 3618.0bp to feature; MODIFIER	silent_mutation	Average:21.697; most accessible tissue: Zhenshan97 young leaf, score: 43.23	N	N	N	N
vg1116562086	T -> C	LOC_Os11g28640-LOC_Os11g28650	intergenic_region ; MODIFIER	silent_mutation	Average:21.697; most accessible tissue: Zhenshan97 young leaf, score: 43.23	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1116562086	5.00E-08	1.01E-07	mr1087	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
vg1116562086	8.58E-06	NA	mr1112	Ind_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
vg1116562086	NA	4.83E-09	mr1595	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
vg1116562086	NA	4.50E-09	mr1600_2	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