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Detailed information for vg1110049605:

Variant ID: vg1110049605 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 10049605
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACTTAAATTAAAACAAATCGCTTGTTTAGAGTTTAGAGGCCATGTGTGCTTGTATAACTTTGTCTAAAAACCAACCTGCTATTTGACGTGTAATTCTTTT[G/A]
CACATTAACGGAAAAAAAACAGCCAACTATGTATATGATGGACAAGACGAAAAGTACTGTGCATCTTCACATGTCAGGAATCTTTTTTTTCCAATGTTTT

Reverse complement sequence

AAAACATTGGAAAAAAAAGATTCCTGACATGTGAAGATGCACAGTACTTTTCGTCTTGTCCATCATATACATAGTTGGCTGTTTTTTTTCCGTTAATGTG[C/T]
AAAAGAATTACACGTCAAATAGCAGGTTGGTTTTTAGACAAAGTTATACAAGCACACATGGCCTCTAAACTCTAAACAAGCGATTTGTTTTAATTTAAGT

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	46.90%	1.90%	3.39%	47.82%	NA
All Indica	2759	23.30%	0.00%	5.00%	71.69%	NA
All Japonica	1512	91.80%	5.60%	0.60%	1.98%	NA
Aus	269	20.40%	0.00%	3.35%	76.21%	NA
Indica I	595	31.60%	0.20%	11.43%	56.81%	NA
Indica II	465	17.00%	0.00%	4.95%	78.06%	NA
Indica III	913	15.30%	0.00%	0.88%	83.79%	NA
Indica Intermediate	786	29.90%	0.00%	4.96%	65.14%	NA
Temperate Japonica	767	97.50%	0.10%	0.39%	1.96%	NA
Tropical Japonica	504	81.30%	14.90%	1.19%	2.58%	NA
Japonica Intermediate	241	95.40%	3.70%	0.00%	0.83%	NA
VI/Aromatic	96	90.60%	0.00%	0.00%	9.38%	NA
Intermediate	90	47.80%	5.60%	4.44%	42.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1110049605	G -> A	LOC_Os11g17900.1	upstream_gene_variant ; 3825.0bp to feature; MODIFIER	silent_mutation	Average:18.437; most accessible tissue: Callus, score: 53.054	N	N	N	N
vg1110049605	G -> A	LOC_Os11g17910.1	upstream_gene_variant ; 2332.0bp to feature; MODIFIER	silent_mutation	Average:18.437; most accessible tissue: Callus, score: 53.054	N	N	N	N
vg1110049605	G -> A	LOC_Os11g17900-LOC_Os11g17910	intergenic_region ; MODIFIER	silent_mutation	Average:18.437; most accessible tissue: Callus, score: 53.054	N	N	N	N
vg1110049605	G -> DEL	N	N	silent_mutation	Average:18.437; most accessible tissue: Callus, score: 53.054	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1110049605	2.85E-09	1.21E-09	mr1794	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
vg1110049605	NA	1.04E-06	mr1121_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