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Detailed information for vg1112750621:

Variant ID: vg1112750621 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 12750621
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

AATCATGCCCTGACGATGTCCTGGGCAAACCAGTGATGAAATCCATTCCGATTTCTTCCCATTTCCATTCCGGGATCTGAAGGGGTTGTAGCAGTCCTGC[G/A]
GGCCTCTGATGTTCTGCTTTGACTCTCTGACAAACATCGCAGAGTGCGACGAATCCGGCTATCTCTCTTCTCATGCTGGCCTACTAGAATTTCTCTTTGA

Reverse complement sequence

TCAAAGAGAAATTCTAGTAGGCCAGCATGAGAAGAGAGATAGCCGGATTCGTCGCACTCTGCGATGTTTGTCAGAGAGTCAAAGCAGAACATCAGAGGCC[C/T]
GCAGGACTGCTACAACCCCTTCAGATCCCGGAATGGAAATGGGAAGAAATCGGAATGGATTTCATCACTGGTTTGCCCAGGACATCGTCAGGGCATGATT

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	56.50%	4.70%	25.35%	13.46%	NA
All Indica	2759	33.30%	6.60%	39.98%	20.08%	NA
All Japonica	1512	94.00%	0.10%	1.26%	4.63%	NA
Aus	269	71.00%	9.70%	18.22%	1.12%	NA
Indica I	595	23.40%	0.30%	33.61%	42.69%	NA
Indica II	465	23.00%	10.30%	50.11%	16.56%	NA
Indica III	913	42.40%	7.10%	41.07%	9.42%	NA
Indica Intermediate	786	36.40%	8.70%	37.53%	17.43%	NA
Temperate Japonica	767	96.60%	0.00%	1.04%	2.35%	NA
Tropical Japonica	504	88.30%	0.20%	1.79%	9.72%	NA
Japonica Intermediate	241	97.50%	0.40%	0.83%	1.24%	NA
VI/Aromatic	96	95.80%	3.10%	1.04%	0.00%	NA
Intermediate	90	53.30%	7.80%	28.89%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1112750621	G -> A	LOC_Os11g22220.1	synonymous_variant ; p.Pro804Pro; LOW	synonymous_codon	Average:11.377; most accessible tissue: Callus, score: 16.702	N	N	N	N
vg1112750621	G -> DEL	LOC_Os11g22220.1	N	frameshift_variant	Average:11.377; most accessible tissue: Callus, score: 16.702	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1112750621	NA	6.72E-06	mr1440_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
vg1112750621	3.12E-06	3.12E-06	mr1440_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