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Detailed information for vg1116629534:

Variant ID: vg1116629534 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 16629534
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGGACAAGCTATATGCTCAGGGGCTTACTAGCTCAAACACAAGTATCATACCTTCAATTTGGACTTGTTCCGGATACATGCAACATGAATTCATGATCAT[A/G]
GGTCTATTTTCTATGCTCAAAGACTGGACCAATTATTATTCCCCGTAAGGGCTATCAACCGAATACTTGCGCCAGTCGGGATTCAATTATTATATTTATT

Reverse complement sequence

AATAAATATAATAATTGAATCCCGACTGGCGCAAGTATTCGGTTGATAGCCCTTACGGGGAATAATAATTGGTCCAGTCTTTGAGCATAGAAAATAGACC[T/C]
ATGATCATGAATTCATGTTGCATGTATCCGGAACAAGTCCAAATTGAAGGTATGATACTTGTGTTTGAGCTAGTAAGCCCCTGAGCATATAGCTTGTCCT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	33.80%	9.60%	49.41%	7.26%	NA
All Indica	2759	7.60%	10.90%	73.72%	7.68%	NA
All Japonica	1512	80.60%	6.50%	4.76%	8.20%	NA
Aus	269	15.20%	15.60%	69.14%	0.00%	NA
Indica I	595	4.00%	19.70%	59.83%	16.47%	NA
Indica II	465	5.60%	2.60%	81.72%	10.11%	NA
Indica III	913	9.10%	8.10%	80.94%	1.86%	NA
Indica Intermediate	786	9.90%	12.60%	71.12%	6.36%	NA
Temperate Japonica	767	91.00%	0.10%	3.78%	5.08%	NA
Tropical Japonica	504	66.90%	17.50%	4.76%	10.91%	NA
Japonica Intermediate	241	75.90%	3.70%	7.88%	12.45%	NA
VI/Aromatic	96	94.80%	0.00%	5.21%	0.00%	NA
Intermediate	90	38.90%	11.10%	42.22%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1116629534	A -> DEL	N	N	silent_mutation	Average:28.13; most accessible tissue: Zhenshan97 root, score: 56.557	N	N	N	N
vg1116629534	A -> G	LOC_Os11g28730-LOC_Os11g28740	intergenic_region ; MODIFIER	silent_mutation	Average:28.13; most accessible tissue: Zhenshan97 root, score: 56.557	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1116629534	5.53E-06	4.94E-79	mr1135	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
vg1116629534	NA	2.89E-07	mr1162	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
vg1116629534	3.29E-06	3.11E-88	mr1504	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
vg1116629534	NA	2.64E-08	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
vg1116629534	NA	3.14E-11	mr1630	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
vg1116629534	NA	1.56E-83	mr1672	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
vg1116629534	NA	1.23E-93	mr1758	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
vg1116629534	NA	6.51E-13	mr1924	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
vg1116629534	NA	8.97E-06	mr1100_2	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
vg1116629534	NA	1.08E-06	mr1758_2	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
vg1116629534	7.24E-06	NA	mr1795_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
vg1116629534	1.63E-09	2.86E-10	mr1795_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
vg1116629534	NA	2.03E-06	mr1888_2	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
vg1116629534	NA	6.64E-07	mr1913_2	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
vg1116629534	4.48E-07	9.08E-07	mr1962_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