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Detailed information for vg0325018273:

Variant ID: vg0325018273 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 25018273
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCAACTTCTAAAATTTCCCAAATCTTGAGATCTATCTAGTGGCACGCTTAGAGGTCTTTAATAGGCTTTATTTTCGCCGTTTGTTGAGTTGTTCCGTTTC[G/A]
CGTGTAGTTCCGGAGCCCGAAGACCCGCAGTGCGAGGATTTCGAGCATCAAGCTCCGGATCGCGAGCAAGGCAAGCCACCTTTGAACATCTTGAGCCTAT

Reverse complement sequence

ATAGGCTCAAGATGTTCAAAGGTGGCTTGCCTTGCTCGCGATCCGGAGCTTGATGCTCGAAATCCTCGCACTGCGGGTCTTCGGGCTCCGGAACTACACG[C/T]
GAAACGGAACAACTCAACAAACGGCGAAAATAAAGCCTATTAAAGACCTCTAAGCGTGCCACTAGATAGATCTCAAGATTTGGGAAATTTTAGAAGTTGA

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	31.70%	8.00%	6.14%	54.08%	NA
All Indica	2759	8.30%	0.90%	5.04%	85.68%	NA
All Japonica	1512	80.60%	16.70%	0.99%	1.65%	NA
Aus	269	5.60%	1.10%	45.72%	47.58%	NA
Indica I	595	15.50%	0.00%	4.03%	80.50%	NA
Indica II	465	2.40%	1.30%	1.51%	94.84%	NA
Indica III	913	3.60%	0.90%	5.81%	89.70%	NA
Indica Intermediate	786	12.00%	1.50%	7.00%	79.52%	NA
Temperate Japonica	767	98.40%	0.40%	0.52%	0.65%	NA
Tropical Japonica	504	47.60%	47.00%	2.18%	3.17%	NA
Japonica Intermediate	241	92.90%	5.40%	0.00%	1.66%	NA
VI/Aromatic	96	3.10%	87.50%	5.21%	4.17%	NA
Intermediate	90	36.70%	15.60%	8.89%	38.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0325018273	G -> A	LOC_Os03g44460.1	downstream_gene_variant ; 3399.0bp to feature; MODIFIER	silent_mutation	Average:7.443; most accessible tissue: Callus, score: 18.01	N	N	N	N
vg0325018273	G -> A	LOC_Os03g44450-LOC_Os03g44460	intergenic_region ; MODIFIER	silent_mutation	Average:7.443; most accessible tissue: Callus, score: 18.01	N	N	N	N
vg0325018273	G -> DEL	N	N	silent_mutation	Average:7.443; most accessible tissue: Callus, score: 18.01	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0325018273	1.06E-06	NA	mr1076	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
vg0325018273	8.70E-08	NA	mr1082	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
vg0325018273	NA	1.56E-06	mr1082	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
vg0325018273	1.70E-06	NA	mr1083	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
vg0325018273	3.75E-07	NA	mr1226	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
vg0325018273	4.36E-06	4.55E-10	mr1408	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
vg0325018273	NA	3.96E-06	mr1408	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
vg0325018273	6.30E-07	NA	mr1411	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
vg0325018273	4.55E-06	NA	mr1560	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
vg0325018273	8.96E-10	NA	mr1082_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
vg0325018273	NA	3.58E-06	mr1082_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
vg0325018273	1.32E-07	NA	mr1083_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
vg0325018273	5.90E-06	NA	mr1103_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
vg0325018273	8.19E-06	NA	mr1104_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
vg0325018273	1.02E-07	NA	mr1107_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
vg0325018273	1.28E-07	NA	mr1226_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
vg0325018273	5.89E-06	5.16E-11	mr1408_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
vg0325018273	NA	7.05E-06	mr1763_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