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Detailed information for vg1218586541:

Variant ID: vg1218586541 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 18586541
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTGGTGTGCCTTCTATTGCCCTTGAGATAATACTCCCATCCTTGAGGGAGCATGGCAAGTGCCGGTACACTATATTATTAAGTCCCTGATCAAACATTTC[T/C]
CGATAGATGTTTGTTAAGACGCAATTGCCGTAAGCAAAGTATGGCCGTCCGATCTTCTGGGTAGGCTGAAGCCCTTGTATAGTGCGCCATTTGCTCCATT

Reverse complement sequence

AATGGAGCAAATGGCGCACTATACAAGGGCTTCAGCCTACCCAGAAGATCGGACGGCCATACTTTGCTTACGGCAATTGCGTCTTAACAAACATCTATCG[A/G]
GAAATGTTTGATCAGGGACTTAATAATATAGTGTACCGGCACTTGCCATGCTCCCTCAAGGATGGGAGTATTATCTCAAGGGCAATAGAAGGCACACCAG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	81.50%	12.70%	0.32%	5.44%	NA
All Indica	2759	77.50%	15.90%	0.36%	6.31%	NA
All Japonica	1512	98.30%	0.70%	0.13%	0.86%	NA
Aus	269	25.30%	53.20%	0.37%	21.19%	NA
Indica I	595	74.10%	24.20%	0.00%	1.68%	NA
Indica II	465	92.50%	7.30%	0.00%	0.22%	NA
Indica III	913	68.60%	18.30%	0.77%	12.38%	NA
Indica Intermediate	786	81.40%	11.80%	0.38%	6.36%	NA
Temperate Japonica	767	99.10%	0.30%	0.00%	0.65%	NA
Tropical Japonica	504	99.00%	0.20%	0.20%	0.60%	NA
Japonica Intermediate	241	94.60%	2.90%	0.41%	2.07%	NA
VI/Aromatic	96	81.20%	8.30%	2.08%	8.33%	NA
Intermediate	90	91.10%	3.30%	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
vg1218586541	T -> C	LOC_Os12g30950.1	synonymous_variant ; p.Arg356Arg; LOW	synonymous_codon	Average:47.082; most accessible tissue: Callus, score: 85.403	N	N	N	N
vg1218586541	T -> DEL	LOC_Os12g30950.1	N	frameshift_variant	Average:47.082; most accessible tissue: Callus, score: 85.403	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1218586541	NA	2.18E-06	mr1006	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
vg1218586541	NA	5.57E-07	mr1052	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
vg1218586541	5.34E-06	5.36E-06	mr1313	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
vg1218586541	1.88E-06	1.88E-06	mr1313	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
vg1218586541	NA	1.18E-06	mr1457	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
vg1218586541	8.33E-07	NA	mr1458	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
vg1218586541	NA	5.26E-10	mr1458	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
vg1218586541	8.28E-06	NA	mr1682	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
vg1218586541	NA	5.91E-07	mr1686	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
vg1218586541	NA	1.33E-06	mr1457_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
vg1218586541	2.52E-07	NA	mr1458_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
vg1218586541	1.85E-06	8.00E-12	mr1458_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
vg1218586541	NA	3.54E-06	mr1899_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