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Detailed information for vg1105740618:

Variant ID: vg1105740618 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 5740618
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGTTCAGGTACTTTATGGTTTTGATTGACGCATCTACTAGATGGTCTCATGTGTGTCTTCTATCGACACGAAACCATGCCTTTGCCAAATTGATGTCACA[A/G]
ATTATAAGGCTGAAGGTAAATTACCCTGAACATAGGATTCAATCAATCCGTATGGACAACGCTGCCGAATTTACATCTCATGCTTTCGATGATTATTGTA

Reverse complement sequence

TACAATAATCATCGAAAGCATGAGATGTAAATTCGGCAGCGTTGTCCATACGGATTGATTGAATCCTATGTTCAGGGTAATTTACCTTCAGCCTTATAAT[T/C]
TGTGACATCAATTTGGCAAAGGCATGGTTTCGTGTCGATAGAAGACACACATGAGACCATCTAGTAGATGCGTCAATCAAAACCATAAAGTACCTGAACG

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	89.20%	10.50%	0.34%	0.00%	NA
All Indica	2759	99.60%	0.40%	0.00%	0.00%	NA
All Japonica	1512	70.20%	29.00%	0.79%	0.00%	NA
Aus	269	98.90%	1.10%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	98.70%	1.30%	0.00%	0.00%	NA
Temperate Japonica	767	86.30%	13.20%	0.52%	0.00%	NA
Tropical Japonica	504	53.00%	46.00%	0.99%	0.00%	NA
Japonica Intermediate	241	55.20%	43.60%	1.24%	0.00%	NA
VI/Aromatic	96	57.30%	38.50%	4.17%	0.00%	NA
Intermediate	90	93.30%	6.70%	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
vg1105740618	A -> G	LOC_Os11g10500.1	synonymous_variant ; p.Gln564Gln; LOW	synonymous_codon	Average:26.95; most accessible tissue: Zhenshan97 flag leaf, score: 36.135	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1105740618	2.95E-06	2.93E-06	mr1258	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
vg1105740618	NA	4.09E-12	mr1871	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