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Detailed information for vg1128161380:

Variant ID: vg1128161380 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 28161380
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.04, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

TAGATTTGTCTTTAAAAGTACTATAATAAAAGTAAACATGCATTTATTTATTGTATATATTATAATAGAAAAATAAGGTCAAAGATATATTTTGTATACC[A/G]
TGTCATTGTCCAAAACGTCAATTAAAATGAAACTGGAGGGAGTAACTAATTAACAAAAAATGGAGTTAACTAAGGTTGGAACAAATCAACAATGCATGTT

Reverse complement sequence

AACATGCATTGTTGATTTGTTCCAACCTTAGTTAACTCCATTTTTTGTTAATTAGTTACTCCCTCCAGTTTCATTTTAATTGACGTTTTGGACAATGACA[T/C]
GGTATACAAAATATATCTTTGACCTTATTTTTCTATTATAATATATACAATAAATAAATGCATGTTTACTTTTATTATAGTACTTTTAAAGACAAATCTA

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	52.50%	14.40%	0.85%	32.18%	NA
All Indica	2759	61.40%	10.60%	0.58%	27.44%	NA
All Japonica	1512	38.50%	15.30%	0.99%	45.24%	NA
Aus	269	51.30%	32.30%	2.23%	14.13%	NA
Indica I	595	55.30%	6.90%	1.01%	36.81%	NA
Indica II	465	83.00%	3.40%	0.43%	13.12%	NA
Indica III	913	54.20%	14.30%	0.44%	31.00%	NA
Indica Intermediate	786	61.50%	13.40%	0.51%	24.68%	NA
Temperate Japonica	767	18.30%	24.30%	1.56%	55.93%	NA
Tropical Japonica	504	63.70%	3.60%	0.40%	32.34%	NA
Japonica Intermediate	241	50.20%	11.20%	0.41%	38.17%	NA
VI/Aromatic	96	22.90%	59.40%	1.04%	16.67%	NA
Intermediate	90	53.30%	15.60%	2.22%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1128161380	A -> DEL	N	N	silent_mutation	Average:11.168; most accessible tissue: Callus, score: 23.379	N	N	N	N
vg1128161380	A -> G	LOC_Os11g46880.1	intron_variant ; MODIFIER	silent_mutation	Average:11.168; most accessible tissue: Callus, score: 23.379	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1128161380	8.98E-06	NA	mr1149_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
vg1128161380	2.83E-08	NA	mr1310_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
vg1128161380	2.29E-06	NA	mr1423_2	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
vg1128161380	2.85E-06	NA	mr1691_2	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
vg1128161380	1.14E-06	NA	mr1945_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
vg1128161380	1.30E-09	NA	mr1959_2	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
vg1128161380	1.06E-06	4.25E-07	mr1959_2	Jap_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