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Detailed information for vg1111565611:

Variant ID: vg1111565611 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 11565611
Reference Allele: T	Alternative Allele: A
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTCTTAAATTACTTATCGAAATCATGATCTGATTGCATCATTAAATTCGTTGCAAATAAATCTTCAAAACAAGACCACACATGGATATCCGACAAAAAAA[T/A]
TTTTTAGTTTATTATTGAATTATTTTTAAATGTTGCACGATGTTCCACCAGATATATCGGAATTGTTTCACTAAGTAGATCGAAAATGTTTCACTCGTTT

Reverse complement sequence

AAACGAGTGAAACATTTTCGATCTACTTAGTGAAACAATTCCGATATATCTGGTGGAACATCGTGCAACATTTAAAAATAATTCAATAATAAACTAAAAA[A/T]
TTTTTTTGTCGGATATCCATGTGTGGTCTTGTTTTGAAGATTTATTTGCAACGAATTTAATGATGCAATCAGATCATGATTTCGATAAGTAATTTAAGAG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	61.60%	37.70%	0.72%	0.00%	NA
All Indica	2759	97.10%	2.30%	0.65%	0.00%	NA
All Japonica	1512	5.80%	93.50%	0.73%	0.00%	NA
Aus	269	31.20%	68.80%	0.00%	0.00%	NA
Indica I	595	96.60%	1.20%	2.18%	0.00%	NA
Indica II	465	99.10%	0.60%	0.22%	0.00%	NA
Indica III	913	97.20%	2.80%	0.00%	0.00%	NA
Indica Intermediate	786	96.10%	3.40%	0.51%	0.00%	NA
Temperate Japonica	767	3.80%	95.40%	0.78%	0.00%	NA
Tropical Japonica	504	10.50%	89.10%	0.40%	0.00%	NA
Japonica Intermediate	241	2.50%	96.30%	1.24%	0.00%	NA
VI/Aromatic	96	6.20%	93.80%	0.00%	0.00%	NA
Intermediate	90	58.90%	35.60%	5.56%	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
vg1111565611	T -> A	LOC_Os11g20070.1	downstream_gene_variant ; 4534.0bp to feature; MODIFIER	silent_mutation	Average:35.317; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg1111565611	T -> A	LOC_Os11g20060-LOC_Os11g20070	intergenic_region ; MODIFIER	silent_mutation	Average:35.317; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1111565611	NA	1.03E-08	mr1047	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
vg1111565611	NA	1.12E-10	mr1336	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
vg1111565611	NA	3.95E-20	mr1580	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
vg1111565611	NA	1.15E-28	mr1793	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
vg1111565611	NA	6.99E-17	mr1825	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
vg1111565611	NA	1.76E-09	mr1198_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
vg1111565611	NA	6.51E-19	mr1218_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
vg1111565611	NA	6.05E-10	mr1228_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
vg1111565611	NA	2.47E-12	mr1325_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
vg1111565611	NA	1.50E-21	mr1401_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
vg1111565611	NA	3.68E-14	mr1579_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
vg1111565611	NA	1.45E-08	mr1751_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
vg1111565611	NA	1.57E-29	mr1825_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