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Detailed information for vg0222546189:

Variant ID: vg0222546189 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 22546189
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TACAATTAGCAAAAGTCTGAATGGTGTAACTGTTCTTCACTTGGGAATTGAAGCTGGAGCTCTGTTGTGCAGAGGACCTCAGCTTGGTTAGCTTGCCGTG[C/G]
ATGAGGGAGAGCAGAGCCTGAGAACTCCCCTCCTTATATGGCTGTGTTTGCTAGGGGAGGATGGGAACATGCATAGTGCGCATGGAAAACGAAGTAGTCC

Reverse complement sequence

GGACTACTTCGTTTTCCATGCGCACTATGCATGTTCCCATCCTCCCCTAGCAAACACAGCCATATAAGGAGGGGAGTTCTCAGGCTCTGCTCTCCCTCAT[G/C]
CACGGCAAGCTAACCAAGCTGAGGTCCTCTGCACAACAGAGCTCCAGCTTCAATTCCCAAGTGAAGAACAGTTACACCATTCAGACTTTTGCTAATTGTA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	39.70%	2.80%	0.78%	56.69%	NA
All Indica	2759	10.20%	4.70%	1.05%	84.09%	NA
All Japonica	1512	96.00%	0.00%	0.07%	3.97%	NA
Aus	269	2.20%	0.00%	1.86%	95.91%	NA
Indica I	595	23.90%	0.20%	1.01%	74.96%	NA
Indica II	465	7.30%	0.20%	0.43%	92.04%	NA
Indica III	913	2.40%	11.60%	0.66%	85.32%	NA
Indica Intermediate	786	10.60%	2.70%	1.91%	84.86%	NA
Temperate Japonica	767	99.30%	0.00%	0.00%	0.65%	NA
Tropical Japonica	504	89.70%	0.00%	0.20%	10.12%	NA
Japonica Intermediate	241	98.30%	0.00%	0.00%	1.66%	NA
VI/Aromatic	96	86.50%	2.10%	0.00%	11.46%	NA
Intermediate	90	61.10%	3.30%	2.22%	33.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0222546189	C -> G	LOC_Os02g37270.1	upstream_gene_variant ; 4390.0bp to feature; MODIFIER	silent_mutation	Average:32.429; most accessible tissue: Callus, score: 82.796	N	N	N	N
vg0222546189	C -> G	LOC_Os02g37280.1	upstream_gene_variant ; 364.0bp to feature; MODIFIER	silent_mutation	Average:32.429; most accessible tissue: Callus, score: 82.796	N	N	N	N
vg0222546189	C -> G	LOC_Os02g37290.1	downstream_gene_variant ; 4792.0bp to feature; MODIFIER	silent_mutation	Average:32.429; most accessible tissue: Callus, score: 82.796	N	N	N	N
vg0222546189	C -> G	LOC_Os02g37280-LOC_Os02g37290	intergenic_region ; MODIFIER	silent_mutation	Average:32.429; most accessible tissue: Callus, score: 82.796	N	N	N	N
vg0222546189	C -> DEL	N	N	silent_mutation	Average:32.429; most accessible tissue: Callus, score: 82.796	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0222546189	NA	2.70E-13	mr1069	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
vg0222546189	NA	2.07E-30	mr1072	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
vg0222546189	NA	4.23E-31	mr1074	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
vg0222546189	NA	7.17E-32	mr1075	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
vg0222546189	NA	3.04E-19	mr1077	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
vg0222546189	3.07E-06	NA	mr1095	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
vg0222546189	4.52E-06	NA	mr1101	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
vg0222546189	2.84E-06	NA	mr1101	Ind_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
vg0222546189	NA	2.12E-41	mr1124	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
vg0222546189	NA	1.08E-15	mr1146	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
vg0222546189	NA	9.78E-27	mr1148	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
vg0222546189	NA	1.85E-13	mr1149	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
vg0222546189	5.01E-06	1.70E-24	mr1150	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
vg0222546189	NA	1.09E-33	mr1202	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
vg0222546189	NA	2.88E-08	mr1222	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
vg0222546189	NA	9.45E-13	mr1441	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
vg0222546189	NA	2.07E-15	mr1592	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
vg0222546189	NA	4.88E-56	mr1861	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
vg0222546189	1.72E-06	NA	mr1868	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
vg0222546189	2.75E-06	NA	mr1868	Ind_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
vg0222546189	7.26E-07	5.99E-07	mr1913	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
vg0222546189	NA	8.83E-24	mr1917	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
vg0222546189	3.56E-06	NA	mr1918	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
vg0222546189	1.19E-06	NA	mr1918	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
vg0222546189	8.05E-06	NA	mr1929	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
vg0222546189	NA	2.61E-59	mr1962	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
vg0222546189	8.33E-06	2.72E-42	mr1072_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
vg0222546189	3.45E-06	7.96E-43	mr1075_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
vg0222546189	1.52E-06	NA	mr1098_2	Ind_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
vg0222546189	4.86E-06	NA	mr1099_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
vg0222546189	1.40E-07	NA	mr1099_2	Ind_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
vg0222546189	2.57E-06	3.06E-58	mr1124_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
vg0222546189	NA	3.22E-29	mr1149_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
vg0222546189	7.69E-06	9.06E-34	mr1150_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
vg0222546189	4.97E-07	NA	mr1150_2	Ind_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
vg0222546189	NA	1.87E-29	mr1441_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
vg0222546189	NA	4.30E-18	mr1592_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
vg0222546189	NA	3.74E-12	mr1595_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
vg0222546189	NA	2.51E-10	mr1600_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
vg0222546189	NA	1.32E-48	mr1861_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
vg0222546189	2.59E-06	NA	mr1918_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
vg0222546189	6.51E-06	NA	mr1929_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
vg0222546189	7.69E-06	NA	mr1962_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