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Detailed information for vg1109865477:

Variant ID: vg1109865477 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 9865477
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTGGCCCCTCCACACAGGTGCCGAACGCGGCTGACATGGCGAAGGCGGCTGCGGTGGCAAGGGCACTCCAGACCAAGGCAGAGATCCTTTCGACAAGCCA[G/A]
CTGCTGGTGCCCCAAGCCGCTCCGTCGCAGTCGGCAGCGGCCCCAACTGCGCTCTCCGCTGTGCAAGCCCAAGTCAACCCTGACCCCGAAACACAAACCG

Reverse complement sequence

CGGTTTGTGTTTCGGGGTCAGGGTTGACTTGGGCTTGCACAGCGGAGAGCGCAGTTGGGGCCGCTGCCGACTGCGACGGAGCGGCTTGGGGCACCAGCAG[C/T]
TGGCTTGTCGAAAGGATCTCTGCCTTGGTCTGGAGTGCCCTTGCCACCGCAGCCGCCTTCGCCATGTCAGCCGCGTTCGGCACCTGTGTGGAGGGGCCAG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	50.30%	5.10%	12.31%	32.35%	NA
All Indica	2759	27.50%	7.70%	15.80%	48.97%	NA
All Japonica	1512	95.80%	0.80%	0.86%	2.58%	NA
Aus	269	31.20%	3.00%	40.52%	25.28%	NA
Indica I	595	31.40%	6.10%	17.48%	45.04%	NA
Indica II	465	23.40%	4.50%	13.33%	58.71%	NA
Indica III	913	21.10%	12.30%	16.21%	50.38%	NA
Indica Intermediate	786	34.40%	5.60%	15.52%	44.53%	NA
Temperate Japonica	767	97.00%	0.00%	0.52%	2.48%	NA
Tropical Japonica	504	94.00%	2.40%	1.39%	2.18%	NA
Japonica Intermediate	241	95.40%	0.00%	0.83%	3.73%	NA
VI/Aromatic	96	40.60%	1.00%	18.75%	39.58%	NA
Intermediate	90	51.10%	5.60%	6.67%	36.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1109865477	G -> A	LOC_Os11g17670.1	synonymous_variant ; p.Gln244Gln; LOW	stop_gained	Average:15.396; most accessible tissue: Callus, score: 29.289	N	N	N	N
vg1109865477	G -> DEL	LOC_Os11g17670.1	N	frameshift_variant	Average:15.396; most accessible tissue: Callus, score: 29.289	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1109865477	1.02E-06	2.56E-06	mr1081	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
vg1109865477	3.73E-06	NA	mr1254	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
vg1109865477	NA	3.41E-06	mr1783	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