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Detailed information for vg1121944084:

Variant ID: vg1121944084 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21944084
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, A: 0.05, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:

AATATATTAGGCGTTTGCTTGATATTCTATGCCTGTTTTAATATCCTGACATAAGGTAGTATCGGGGTATTTGCCGATACATGCTAGATCTATATGATCG[G/A]
CTATGCTGTAAGCTTATATAGTCTTGTTATTAGTATATATTTCGGTCTAAGTGATTCATTCTGTCTCGGCATGGCGACGATCTATCCCAGTCACTTGATT

Reverse complement sequence

AATCAAGTGACTGGGATAGATCGTCGCCATGCCGAGACAGAATGAATCACTTAGACCGAAATATATACTAATAACAAGACTATATAAGCTTACAGCATAG[C/T]
CGATCATATAGATCTAGCATGTATCGGCAAATACCCCGATACTACCTTATGTCAGGATATTAAAACAGGCATAGAATATCAAGCAAACGCCTAATATATT

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	57.20%	37.70%	0.28%	4.89%	NA
All Indica	2759	40.50%	55.30%	0.43%	3.81%	NA
All Japonica	1512	84.00%	13.60%	0.07%	2.38%	NA
Aus	269	72.90%	2.60%	0.00%	24.54%	NA
Indica I	595	76.10%	23.70%	0.00%	0.17%	NA
Indica II	465	35.70%	62.80%	1.08%	0.43%	NA
Indica III	913	24.20%	68.00%	0.44%	7.34%	NA
Indica Intermediate	786	35.20%	59.90%	0.38%	4.45%	NA
Temperate Japonica	767	94.10%	5.60%	0.00%	0.26%	NA
Tropical Japonica	504	67.30%	27.40%	0.00%	5.36%	NA
Japonica Intermediate	241	86.70%	10.00%	0.41%	2.90%	NA
VI/Aromatic	96	69.80%	11.50%	0.00%	18.75%	NA
Intermediate	90	57.80%	35.60%	0.00%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121944084	G -> A	LOC_Os11g37170.1	upstream_gene_variant ; 463.0bp to feature; MODIFIER	silent_mutation	Average:19.435; most accessible tissue: Callus, score: 25.871	N	N	N	N
vg1121944084	G -> A	LOC_Os11g37160-LOC_Os11g37170	intergenic_region ; MODIFIER	silent_mutation	Average:19.435; most accessible tissue: Callus, score: 25.871	N	N	N	N
vg1121944084	G -> DEL	N	N	silent_mutation	Average:19.435; most accessible tissue: Callus, score: 25.871	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121944084	NA	1.20E-06	mr1698	Jap_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
vg1121944084	NA	9.28E-07	mr1517_2	Jap_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
vg1121944084	4.77E-06	2.62E-06	mr1715_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