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Detailed information for vg1112940954:

Variant ID: vg1112940954 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 12940954
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.08, others allele: 0.00, population size: 59. )

Flanking Sequence (100 bp) in Reference Genome:

CAATCTGGGCACGATTTGCTGAAATCCAAGCCTTAATCCCGGAAGATCTAGCGAACATCATTACTCCAGCTATATACCTCGAGCAACATCAATTCAAGCT[A/G]
GAGAAGGCTCAGCAACGGATAGCCGATCGGCGGGAGCGGAAAGTCATTGAAGCTACCATCCAAGCCAATCGGCAACTCGTGCATGAAGAGAAAGCCAAGC

Reverse complement sequence

GCTTGGCTTTCTCTTCATGCACGAGTTGCCGATTGGCTTGGATGGTAGCTTCAATGACTTTCCGCTCCCGCCGATCGGCTATCCGTTGCTGAGCCTTCTC[T/C]
AGCTTGAATTGATGTTGCTCGAGGTATATAGCTGGAGTAATGATGTTCGCTAGATCTTCCGGGATTAAGGCTTGGATTTCAGCAAATCGTGCCCAGATTG

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	46.50%	14.50%	6.73%	32.23%	NA
All Indica	2759	22.70%	15.00%	10.80%	51.54%	NA
All Japonica	1512	95.40%	1.30%	0.60%	2.65%	NA
Aus	269	1.50%	84.80%	3.35%	10.41%	NA
Indica I	595	42.20%	15.50%	5.04%	37.31%	NA
Indica II	465	18.50%	7.30%	10.11%	64.09%	NA
Indica III	913	14.90%	15.10%	14.57%	55.42%	NA
Indica Intermediate	786	19.30%	19.10%	11.20%	50.38%	NA
Temperate Japonica	767	97.00%	1.80%	0.00%	1.17%	NA
Tropical Japonica	504	91.90%	1.20%	1.59%	5.36%	NA
Japonica Intermediate	241	97.90%	0.00%	0.41%	1.66%	NA
VI/Aromatic	96	88.50%	10.40%	0.00%	1.04%	NA
Intermediate	90	45.60%	16.70%	2.22%	35.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1112940954	A -> DEL	LOC_Os11g22510.1	N	frameshift_variant	Average:12.57; most accessible tissue: Callus, score: 61.595	N	N	N	N
vg1112940954	A -> G	LOC_Os11g22510.1	synonymous_variant ; p.Leu547Leu; LOW	synonymous_codon	Average:12.57; most accessible tissue: Callus, score: 61.595	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1112940954	NA	6.63E-07	mr1073	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
vg1112940954	NA	5.86E-06	mr1434	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
vg1112940954	NA	8.24E-06	mr1884	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
vg1112940954	1.88E-06	1.88E-06	mr1126_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