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Detailed information for vg1125323327:

Variant ID: vg1125323327 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25323327
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCCTCTACTGCTCCTTGTTCCCATATCATCACATCTTTGATACTGACGAGATGATTAGCCTGATGGTTGCTGAAGGTTTAACACAGACTACAAGCAGGGA[A/G]
GCCCAAGTGGATGGTGATATCAGCAGGCTTCAGAGTGAATGCTTTGATCTTGTCAATAATCCTGGGTCTAATGGGGGAATCAGAAGAGGATGCATGATGC

Reverse complement sequence

GCATCATGCATCCTCTTCTGATTCCCCCATTAGACCCAGGATTATTGACAAGATCAAAGCATTCACTCTGAAGCCTGCTGATATCACCATCCACTTGGGC[T/C]
TCCCTGCTTGTAGTCTGTGTTAAACCTTCAGCAACCATCAGGCTAATCATCTCGTCAGTATCAAAGATGTGATGATATGGGAACAAGGAGCAGTAGAGGA

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	55.40%	15.90%	0.28%	28.44%	NA
All Indica	2759	80.00%	3.40%	0.22%	16.42%	NA
All Japonica	1512	17.50%	35.30%	0.33%	46.83%	NA
Aus	269	38.70%	21.20%	0.00%	40.15%	NA
Indica I	595	51.40%	3.90%	0.50%	44.20%	NA
Indica II	465	77.60%	1.70%	0.22%	20.43%	NA
Indica III	913	93.60%	3.60%	0.00%	2.74%	NA
Indica Intermediate	786	87.20%	3.70%	0.25%	8.91%	NA
Temperate Japonica	767	4.20%	55.00%	0.39%	40.42%	NA
Tropical Japonica	504	35.90%	9.50%	0.40%	54.17%	NA
Japonica Intermediate	241	21.60%	26.60%	0.00%	51.87%	NA
VI/Aromatic	96	3.10%	54.20%	1.04%	41.67%	NA
Intermediate	90	44.40%	15.60%	1.11%	38.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1125323327	A -> DEL	LOC_Os11g42070.1	N	frameshift_variant	Average:64.426; most accessible tissue: Callus, score: 76.545	N	N	N	N
vg1125323327	A -> DEL	LOC_Os11g42070.2	N	frameshift_variant	Average:64.426; most accessible tissue: Callus, score: 76.545	N	N	N	N
vg1125323327	A -> G	LOC_Os11g42070.1	synonymous_variant ; p.Glu495Glu; LOW	synonymous_codon	Average:64.426; most accessible tissue: Callus, score: 76.545	N	N	N	N
vg1125323327	A -> G	LOC_Os11g42070.2	synonymous_variant ; p.Glu495Glu; LOW	synonymous_codon	Average:64.426; most accessible tissue: Callus, score: 76.545	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125323327	NA	4.33E-09	mr1662	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
vg1125323327	NA	7.07E-06	mr1191_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
vg1125323327	NA	2.30E-06	mr1543_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
vg1125323327	4.71E-07	4.89E-07	mr1662_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
vg1125323327	2.73E-09	3.04E-14	mr1662_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
vg1125323327	NA	4.43E-06	mr1745_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