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Detailed information for vg1124342509:

Variant ID: vg1124342509 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24342509
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.91, T: 0.11, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

GCCACATATGACTAAATAGCGAGGTGCAAGAGAAAAGAAGGATGAGAGAGAAATAGTCACCTCTCATGCAATAGGCAACCCCTACACAAACTTCAATAAA[C/T]
ATGTGAGAGTATTAGAGATATTGAGAATTGTGTGGTAGAGGTAACCTATTATATATATCACCTCTTAATTTAATTATGTATGTCATACATGAAATTGGAT

Reverse complement sequence

ATCCAATTTCATGTATGACATACATAATTAAATTAAGAGGTGATATATATAATAGGTTACCTCTACCACACAATTCTCAATATCTCTAATACTCTCACAT[G/A]
TTTATTGAAGTTTGTGTAGGGGTTGCCTATTGCATGAGAGGTGACTATTTCTCTCTCATCCTTCTTTTCTCTTGCACCTCGCTATTTAGTCATATGTGGC

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	85.00%	14.90%	0.11%	0.00%	NA
All Indica	2759	84.30%	15.50%	0.14%	0.00%	NA
All Japonica	1512	98.30%	1.70%	0.00%	0.00%	NA
Aus	269	15.60%	84.40%	0.00%	0.00%	NA
Indica I	595	90.30%	9.40%	0.34%	0.00%	NA
Indica II	465	88.20%	11.80%	0.00%	0.00%	NA
Indica III	913	77.50%	22.50%	0.00%	0.00%	NA
Indica Intermediate	786	85.50%	14.20%	0.25%	0.00%	NA
Temperate Japonica	767	99.50%	0.50%	0.00%	0.00%	NA
Tropical Japonica	504	96.80%	3.20%	0.00%	0.00%	NA
Japonica Intermediate	241	97.50%	2.50%	0.00%	0.00%	NA
VI/Aromatic	96	84.40%	14.60%	1.04%	0.00%	NA
Intermediate	90	91.10%	8.90%	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
vg1124342509	C -> T	LOC_Os11g40700-LOC_Os11g40720	intergenic_region ; MODIFIER	silent_mutation	Average:44.659; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124342509	5.31E-09	4.49E-10	mr1238	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
vg1124342509	2.34E-06	7.55E-07	mr1309	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
vg1124342509	NA	2.52E-06	mr1484	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
vg1124342509	7.70E-07	3.87E-08	mr1238_2	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
vg1124342509	1.36E-07	7.63E-09	mr1484_2	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
vg1124342509	NA	5.85E-06	mr1522_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
vg1124342509	7.58E-09	7.72E-11	mr1841_2	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
vg1124342509	1.58E-08	1.58E-08	mr1945_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