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Detailed information for vg1127982448:

Variant ID: vg1127982448 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 27982448
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.92, G: 0.08, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:

ATAACTTCTACAAAACCAAATTAATTGCCCCAAAAATCTCACTATTAATTTGTTTTAATACGTAGAAAATAACGGGTATTTGGCTAGTATAGTAGTATGT[G/A]
CCAATTGTGTAGCTGAATTGGTAGCTTGTGTAGCTTAATTATAAGCAATTGTAAAAAAAAATGAGCAAATTGTGTAGCTGAATTATACATTGTAAAAAAA

Reverse complement sequence

TTTTTTTACAATGTATAATTCAGCTACACAATTTGCTCATTTTTTTTTACAATTGCTTATAATTAAGCTACACAAGCTACCAATTCAGCTACACAATTGG[C/T]
ACATACTACTATACTAGCCAAATACCCGTTATTTTCTACGTATTAAAACAAATTAATAGTGAGATTTTTGGGGCAATTAATTTGGTTTTGTAGAAGTTAT

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	40.80%	15.10%	1.90%	42.21%	NA
All Indica	2759	56.80%	4.70%	1.30%	37.15%	NA
All Japonica	1512	15.40%	29.10%	1.98%	53.51%	NA
Aus	269	28.30%	42.40%	7.06%	22.30%	NA
Indica I	595	50.30%	7.20%	1.18%	41.34%	NA
Indica II	465	40.40%	7.10%	1.29%	51.18%	NA
Indica III	913	71.30%	0.20%	0.22%	28.26%	NA
Indica Intermediate	786	54.60%	6.70%	2.67%	36.01%	NA
Temperate Japonica	767	12.10%	22.30%	0.78%	64.80%	NA
Tropical Japonica	504	22.40%	36.10%	2.18%	39.29%	NA
Japonica Intermediate	241	11.20%	36.10%	5.39%	47.30%	NA
VI/Aromatic	96	17.70%	8.30%	3.12%	70.83%	NA
Intermediate	90	36.70%	24.40%	2.22%	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
vg1127982448	G -> A	LOC_Os11g46210.1	upstream_gene_variant ; 2249.0bp to feature; MODIFIER	silent_mutation	Average:21.605; most accessible tissue: Callus, score: 81.564	N	N	N	N
vg1127982448	G -> A	LOC_Os11g46200.1	intron_variant ; MODIFIER	silent_mutation	Average:21.605; most accessible tissue: Callus, score: 81.564	N	N	N	N
vg1127982448	G -> DEL	N	N	silent_mutation	Average:21.605; most accessible tissue: Callus, score: 81.564	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1127982448	NA	5.30E-06	mr1345	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
vg1127982448	1.25E-07	1.25E-07	mr1459	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
vg1127982448	6.67E-07	NA	mr1745	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
vg1127982448	NA	5.28E-06	mr1759	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