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Detailed information for vg1126329911:

Variant ID: vg1126329911 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 26329911
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTGGAGGCCGGATCCAGTGGCGGCTGTTGGGTGGGCGTTGGAAGGCGACGCGGGCGGATCCGAGGTTTGTGGGCGTAGAAGCTGGTGGCGCCGTCGATGG[A/T]
GGCGGTCGCTCGTCGTCTTCATCGCAGCCGCCGTCAACATCGTCGTCGTCGTTGTCGCAGCTACCGCCACCATGGCCGCTCGCTCCTGCCTGCCTAAGCC

Reverse complement sequence

GGCTTAGGCAGGCAGGAGCGAGCGGCCATGGTGGCGGTAGCTGCGACAACGACGACGACGATGTTGACGGCGGCTGCGATGAAGACGACGAGCGACCGCC[T/A]
CCATCGACGGCGCCACCAGCTTCTACGCCCACAAACCTCGGATCCGCCCGCGTCGCCTTCCAACGCCCACCCAACAGCCGCCACTGGATCCGGCCTCCAC

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	94.30%	5.40%	0.32%	0.00%	NA
All Indica	2759	93.40%	6.10%	0.51%	0.00%	NA
All Japonica	1512	95.70%	4.30%	0.00%	0.00%	NA
Aus	269	94.80%	5.20%	0.00%	0.00%	NA
Indica I	595	98.80%	1.20%	0.00%	0.00%	NA
Indica II	465	95.50%	4.10%	0.43%	0.00%	NA
Indica III	913	94.60%	4.30%	1.10%	0.00%	NA
Indica Intermediate	786	86.60%	13.10%	0.25%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	89.10%	10.90%	0.00%	0.00%	NA
Japonica Intermediate	241	96.70%	3.30%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	7.80%	1.11%	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
vg1126329911	A -> T	LOC_Os11g43650.1	synonymous_variant ; p.Gly33Gly; LOW	synonymous_codon	Average:42.645; most accessible tissue: Zhenshan97 panicle, score: 84.824	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1126329911	3.77E-07	3.13E-08	mr1133	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
vg1126329911	NA	7.40E-08	mr1133_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
vg1126329911	NA	4.64E-07	mr1667_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