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Detailed information for vg0321323667:

Variant ID: vg0321323667 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 21323667
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATAAGGGTTGGTCTTGCCCTCTACAGGCCCTTCTCCACGCCCAACTCGGGATAGAAACCAAAGGAAACACGAAACATGCCTTCTCGAGCAATGAAACCC[G/A]
AGACCCGACGACAATAGACTCTGACTCGGACCCTGCCGGTCTGACCGCCCACATACTTGAGGTCAGACCGGCCCTACTAGCCGGTCAGACCGCCCACACA

Reverse complement sequence

TGTGTGGGCGGTCTGACCGGCTAGTAGGGCCGGTCTGACCTCAAGTATGTGGGCGGTCAGACCGGCAGGGTCCGAGTCAGAGTCTATTGTCGTCGGGTCT[C/T]
GGGTTTCATTGCTCGAGAAGGCATGTTTCGTGTTTCCTTTGGTTTCTATCCCGAGTTGGGCGTGGAGAAGGGCCTGTAGAGGGCAAGACCAACCCTTATT

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	60.60%	33.70%	0.40%	5.27%	NA
All Indica	2759	95.20%	3.70%	0.36%	0.69%	NA
All Japonica	1512	7.50%	91.60%	0.00%	0.93%	NA
Aus	269	1.50%	16.40%	3.35%	78.81%	NA
Indica I	595	94.60%	5.40%	0.00%	0.00%	NA
Indica II	465	97.20%	2.60%	0.22%	0.00%	NA
Indica III	913	96.70%	2.20%	0.77%	0.33%	NA
Indica Intermediate	786	92.70%	5.00%	0.25%	2.04%	NA
Temperate Japonica	767	0.50%	99.50%	0.00%	0.00%	NA
Tropical Japonica	504	6.20%	91.10%	0.00%	2.78%	NA
Japonica Intermediate	241	32.40%	67.60%	0.00%	0.00%	NA
VI/Aromatic	96	76.00%	22.90%	0.00%	1.04%	NA
Intermediate	90	53.30%	43.30%	0.00%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0321323667	G -> A	LOC_Os03g38410.1	upstream_gene_variant ; 1343.0bp to feature; MODIFIER	silent_mutation	Average:56.158; most accessible tissue: Minghui63 flag leaf, score: 73.752	N	N	N	N
vg0321323667	G -> A	LOC_Os03g38410-LOC_Os03g38430	intergenic_region ; MODIFIER	silent_mutation	Average:56.158; most accessible tissue: Minghui63 flag leaf, score: 73.752	N	N	N	N
vg0321323667	G -> DEL	N	N	silent_mutation	Average:56.158; most accessible tissue: Minghui63 flag leaf, score: 73.752	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0321323667	NA	4.36E-08	mr1666	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
vg0321323667	NA	1.01E-06	mr1761	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
vg0321323667	NA	1.41E-28	mr1793	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
vg0321323667	NA	2.45E-37	mr1828	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
vg0321323667	NA	2.67E-06	mr1020_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
vg0321323667	NA	3.00E-31	mr1102_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
vg0321323667	NA	2.27E-09	mr1198_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
vg0321323667	NA	6.16E-10	mr1349_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
vg0321323667	NA	3.73E-24	mr1350_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
vg0321323667	NA	1.23E-15	mr1666_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
vg0321323667	NA	2.11E-19	mr1731_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
vg0321323667	7.93E-07	NA	mr1750_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
vg0321323667	NA	2.43E-12	mr1761_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
vg0321323667	NA	7.32E-20	mr1922_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
vg0321323667	NA	9.70E-22	mr1924_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