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Detailed information for vg1118447476:

Variant ID: vg1118447476 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 18447476
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAGTTCACGTTAAAATTAAAAATTTGGTTGAAATTGGAACGATGTGACGGAAAAATTAAAAGTTTGTATGTAGAAAAGTTTTGATGTGATGAAAAAGTTG[G/A]
AAGTTTGAAGAAAAAGTTTAGAACTAAACTCGGCCTAACTGCAAACATGCTTGCACTATCCTTGATGGTGTAAAGTTTCAAACACAATCCAAGCCATGGC

Reverse complement sequence

GCCATGGCTTGGATTGTGTTTGAAACTTTACACCATCAAGGATAGTGCAAGCATGTTTGCAGTTAGGCCGAGTTTAGTTCTAAACTTTTTCTTCAAACTT[C/T]
CAACTTTTTCATCACATCAAAACTTTTCTACATACAAACTTTTAATTTTTCCGTCACATCGTTCCAATTTCAACCAAATTTTTAATTTTAACGTGAACTA

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	90.50%	7.70%	1.31%	0.47%	NA
All Indica	2759	91.20%	7.40%	0.62%	0.80%	NA
All Japonica	1512	92.10%	6.60%	1.32%	0.00%	NA
Aus	269	71.40%	19.70%	8.92%	0.00%	NA
Indica I	595	99.30%	0.70%	0.00%	0.00%	NA
Indica II	465	98.30%	1.70%	0.00%	0.00%	NA
Indica III	913	82.90%	13.90%	1.10%	2.08%	NA
Indica Intermediate	786	90.60%	8.10%	0.89%	0.38%	NA
Temperate Japonica	767	97.70%	0.00%	2.35%	0.00%	NA
Tropical Japonica	504	81.30%	18.30%	0.40%	0.00%	NA
Japonica Intermediate	241	96.70%	3.30%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	8.90%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1118447476	G -> A	LOC_Os11g31560.1	upstream_gene_variant ; 1826.0bp to feature; MODIFIER	silent_mutation	Average:50.393; most accessible tissue: Callus, score: 96.839	N	N	N	N
vg1118447476	G -> A	LOC_Os11g31570.1	downstream_gene_variant ; 817.0bp to feature; MODIFIER	silent_mutation	Average:50.393; most accessible tissue: Callus, score: 96.839	N	N	N	N
vg1118447476	G -> A	LOC_Os11g31570.2	downstream_gene_variant ; 817.0bp to feature; MODIFIER	silent_mutation	Average:50.393; most accessible tissue: Callus, score: 96.839	N	N	N	N
vg1118447476	G -> A	LOC_Os11g31560-LOC_Os11g31570	intergenic_region ; MODIFIER	silent_mutation	Average:50.393; most accessible tissue: Callus, score: 96.839	N	N	N	N
vg1118447476	G -> DEL	N	N	silent_mutation	Average:50.393; most accessible tissue: Callus, score: 96.839	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1118447476	NA	1.24E-07	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
vg1118447476	NA	3.70E-07	mr1808_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
vg1118447476	NA	1.87E-07	mr1808_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
vg1118447476	3.64E-06	6.50E-06	mr1928_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