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Detailed information for vg1219590404:

Variant ID: vg1219590404 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 19590404
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAAAATGAGGTCCTTCACTGTAGTAGAACTGTCAGGCTATAAAAGTTACCACTAGCAAAACTTTATGGTTGCCTGCAGGCTGGCTGGCCAAGGCAGAGCT[A/G]
CATAGCGCAGAACTGCAAGGAGTAGCTAGCTAGTAGGTACGTGTCGACATGCCACAGGGCAGAGGCGCACAGCACAATAATCGATCGGCGAAAGAGCTCC

Reverse complement sequence

GGAGCTCTTTCGCCGATCGATTATTGTGCTGTGCGCCTCTGCCCTGTGGCATGTCGACACGTACCTACTAGCTAGCTACTCCTTGCAGTTCTGCGCTATG[T/C]
AGCTCTGCCTTGGCCAGCCAGCCTGCAGGCAACCATAAAGTTTTGCTAGTGGTAACTTTTATAGCCTGACAGTTCTACTACAGTGAAGGACCTCATTTTA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	38.20%	7.40%	0.68%	53.70%	NA
All Indica	2759	4.80%	4.70%	1.09%	89.42%	NA
All Japonica	1512	96.80%	0.90%	0.00%	2.31%	NA
Aus	269	27.10%	68.80%	0.37%	3.72%	NA
Indica I	595	4.20%	0.30%	0.50%	94.96%	NA
Indica II	465	3.40%	2.40%	1.94%	92.26%	NA
Indica III	913	3.40%	7.70%	0.88%	88.06%	NA
Indica Intermediate	786	7.80%	5.90%	1.27%	85.11%	NA
Temperate Japonica	767	98.20%	0.40%	0.00%	1.43%	NA
Tropical Japonica	504	96.40%	0.40%	0.00%	3.17%	NA
Japonica Intermediate	241	92.90%	3.70%	0.00%	3.32%	NA
VI/Aromatic	96	82.30%	14.60%	0.00%	3.12%	NA
Intermediate	90	63.30%	10.00%	1.11%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1219590404	A -> DEL	N	N	silent_mutation	Average:15.387; most accessible tissue: Callus, score: 95.855	N	N	N	N
vg1219590404	A -> G	LOC_Os12g32450-LOC_Os12g32470	intergenic_region ; MODIFIER	silent_mutation	Average:15.387; most accessible tissue: Callus, score: 95.855	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1219590404	NA	4.38E-06	mr1545	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
vg1219590404	NA	2.89E-06	mr1808	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
vg1219590404	9.13E-07	NA	mr1045_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
vg1219590404	NA	9.06E-09	mr1166_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
vg1219590404	3.59E-07	7.13E-06	mr1206_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
vg1219590404	2.63E-06	1.41E-06	mr1206_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
vg1219590404	8.50E-06	NA	mr1308_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
vg1219590404	2.81E-06	NA	mr1381_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
vg1219590404	3.45E-06	2.18E-06	mr1381_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
vg1219590404	7.87E-06	NA	mr1578_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
vg1219590404	6.66E-07	NA	mr1581_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
vg1219590404	2.64E-06	NA	mr1730_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
vg1219590404	NA	5.88E-06	mr1735_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
vg1219590404	NA	1.10E-15	mr1846_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
vg1219590404	NA	9.75E-06	mr1862_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
vg1219590404	5.26E-06	NA	mr1866_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
vg1219590404	6.06E-07	NA	mr1901_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
vg1219590404	9.13E-06	9.12E-06	mr1906_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
vg1219590404	3.21E-07	6.88E-10	mr1909_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
vg1219590404	NA	3.76E-06	mr1909_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
vg1219590404	NA	1.36E-08	mr1921_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
vg1219590404	1.19E-06	NA	mr1938_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
vg1219590404	5.38E-06	5.38E-06	mr1941_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
vg1219590404	NA	7.46E-06	mr1943_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
vg1219590404	NA	4.10E-06	mr1951_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
vg1219590404	8.35E-06	8.35E-06	mr1953_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