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Detailed information for vg1116826188:

Variant ID: vg1116826188 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 16826188
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.08, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:

GGCCATGGGCAACCTCGAAAGGCTTGATATGAAGTTCAACACGCTGGAAGGCGTCTTCGGCATGGATAACCTCGCGAGCCTTCGTGAGGTGCACATGACG[G/A]
CCGGTGAAAAAGCCGGTGAGATCACCAAGTCAATAGTGCGTGAGCTGGAGGCCGAGGCAGGTAAATACGCCAATACACCAAGAGTGGTCGTTTACGAGTT

Reverse complement sequence

AACTCGTAAACGACCACTCTTGGTGTATTGGCGTATTTACCTGCCTCGGCCTCCAGCTCACGCACTATTGACTTGGTGATCTCACCGGCTTTTTCACCGG[C/T]
CGTCATGTGCACCTCACGAAGGCTCGCGAGGTTATCCATGCCGAAGACGCCTTCCAGCGTGTTGAACTTCATATCAAGCCTTTCGAGGTTGCCCATGGCC

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	37.30%	30.00%	0.40%	32.29%	NA
All Indica	2759	6.90%	49.80%	0.58%	42.73%	NA
All Japonica	1512	92.90%	1.10%	0.07%	6.02%	NA
Aus	269	13.80%	0.40%	0.74%	85.13%	NA
Indica I	595	13.10%	67.10%	0.17%	19.66%	NA
Indica II	465	1.90%	49.00%	0.22%	48.82%	NA
Indica III	913	3.30%	40.60%	0.99%	55.09%	NA
Indica Intermediate	786	9.20%	48.00%	0.64%	42.24%	NA
Temperate Japonica	767	96.70%	1.20%	0.13%	1.96%	NA
Tropical Japonica	504	89.10%	1.00%	0.00%	9.92%	NA
Japonica Intermediate	241	88.40%	0.80%	0.00%	10.79%	NA
VI/Aromatic	96	93.80%	2.10%	0.00%	4.17%	NA
Intermediate	90	46.70%	27.80%	0.00%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1116826188	G -> A	LOC_Os11g29050.1	missense_variant ; p.Ala702Thr; MODERATE	nonsynonymous_codon ; A702T	Average:38.917; most accessible tissue: Callus, score: 90.953	unknown	unknown	DELETERIOUS	0.01
vg1116826188	G -> DEL	LOC_Os11g29050.1	N	frameshift_variant	Average:38.917; most accessible tissue: Callus, score: 90.953	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1116826188	NA	4.05E-06	mr1060_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
vg1116826188	NA	8.17E-09	mr1172_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
vg1116826188	NA	8.64E-06	mr1346_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
vg1116826188	9.52E-06	2.24E-06	mr1346_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
vg1116826188	NA	4.64E-06	mr1380_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
vg1116826188	NA	3.38E-07	mr1428_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
vg1116826188	9.52E-06	9.52E-06	mr1456_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
vg1116826188	NA	1.37E-06	mr1579_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
vg1116826188	NA	1.11E-06	mr1996_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