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Detailed information for vg1122418723:

Variant ID: vg1122418723 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 22418723
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAGCCATCCCTGTTGAACTATAAAGCTTCAAAGAGCAGCAAGCAGAGGATACACACACCAGAGTACCTGATAGGGATGCAAGTGGGCAAGCCCACTACCC[G/A]
TATAAAAACTCGCTTGCGAGTTCAGTTTTCAACTTTTTATATGATAGTATAAAATTTAGAAGAAAATATGAACTAGAAGTGGGATAAGCGGCAAAACAAA

Reverse complement sequence

TTTGTTTTGCCGCTTATCCCACTTCTAGTTCATATTTTCTTCTAAATTTTATACTATCATATAAAAAGTTGAAAACTGAACTCGCAAGCGAGTTTTTATA[C/T]
GGGTAGTGGGCTTGCCCACTTGCATCCCTATCAGGTACTCTGGTGTGTGTATCCTCTGCTTGCTGCTCTTTGAAGCTTTATAGTTCAACAGGGATGGCTG

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	83.40%	11.30%	0.25%	4.99%	NA
All Indica	2759	94.60%	0.50%	0.33%	4.57%	NA
All Japonica	1512	61.00%	33.80%	0.13%	5.03%	NA
Aus	269	87.70%	1.50%	0.37%	10.41%	NA
Indica I	595	95.30%	0.00%	0.34%	4.37%	NA
Indica II	465	97.60%	0.60%	0.00%	1.72%	NA
Indica III	913	92.00%	0.20%	0.66%	7.12%	NA
Indica Intermediate	786	95.40%	1.00%	0.13%	3.44%	NA
Temperate Japonica	767	85.80%	9.60%	0.26%	4.30%	NA
Tropical Japonica	504	25.40%	66.90%	0.00%	7.74%	NA
Japonica Intermediate	241	56.80%	41.50%	0.00%	1.66%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	85.60%	8.90%	0.00%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1122418723	G -> A	LOC_Os11g37850.1	upstream_gene_variant ; 545.0bp to feature; MODIFIER	silent_mutation	Average:71.427; most accessible tissue: Callus, score: 91.941	N	N	N	N
vg1122418723	G -> A	LOC_Os11g37840.1	downstream_gene_variant ; 4488.0bp to feature; MODIFIER	silent_mutation	Average:71.427; most accessible tissue: Callus, score: 91.941	N	N	N	N
vg1122418723	G -> A	LOC_Os11g37840-LOC_Os11g37850	intergenic_region ; MODIFIER	silent_mutation	Average:71.427; most accessible tissue: Callus, score: 91.941	N	N	N	N
vg1122418723	G -> DEL	N	N	silent_mutation	Average:71.427; most accessible tissue: Callus, score: 91.941	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1122418723	NA	4.01E-07	mr1668	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
vg1122418723	NA	8.66E-16	mr1871	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
vg1122418723	NA	4.32E-06	mr1871	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
vg1122418723	7.12E-07	4.76E-23	mr1042_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
vg1122418723	NA	5.63E-07	mr1042_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
vg1122418723	NA	3.45E-08	mr1084_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
vg1122418723	NA	4.47E-06	mr1206_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
vg1122418723	NA	1.48E-08	mr1502_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
vg1122418723	NA	6.37E-09	mr1668_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
vg1122418723	NA	7.98E-29	mr1699_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
vg1122418723	7.41E-06	6.65E-16	mr1742_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
vg1122418723	NA	2.91E-08	mr1765_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
vg1122418723	6.74E-10	3.14E-28	mr1871_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
vg1122418723	NA	3.71E-09	mr1871_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