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Detailed information for vg0321841885:

Variant ID: vg0321841885 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 21841885
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACCCAGGCCAACCCTTCCACATTTTAGTTGTTAATCAAGTTTTAAGAAGTAAACCACTAACTTAGGTACATTGCTAGGCTTGCCCGTAACCGAGGGCGCG[A/G]
CTATTCGAATAGATTATACTCTGATCAGAGGTGTACATCTTTACCCACAAGACACGTCTTCCTCACGTGTAACCACGCACAACATACCACCACGGCATAC

Reverse complement sequence

GTATGCCGTGGTGGTATGTTGTGCGTGGTTACACGTGAGGAAGACGTGTCTTGTGGGTAAAGATGTACACCTCTGATCAGAGTATAATCTATTCGAATAG[T/C]
CGCGCCCTCGGTTACGGGCAAGCCTAGCAATGTACCTAAGTTAGTGGTTTACTTCTTAAAACTTGATTAACAACTAAAATGTGGAAGGGTTGGCCTGGGT

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	54.90%	0.60%	24.57%	19.95%	NA
All Indica	2759	34.90%	0.70%	34.80%	29.61%	NA
All Japonica	1512	91.90%	0.40%	7.01%	0.73%	NA
Aus	269	31.20%	0.00%	29.37%	39.41%	NA
Indica I	595	33.90%	0.50%	30.76%	34.79%	NA
Indica II	465	48.80%	0.40%	26.67%	24.09%	NA
Indica III	913	25.20%	1.20%	42.94%	30.67%	NA
Indica Intermediate	786	38.70%	0.40%	33.21%	27.74%	NA
Temperate Japonica	767	99.30%	0.00%	0.65%	0.00%	NA
Tropical Japonica	504	92.30%	0.60%	4.96%	2.18%	NA
Japonica Intermediate	241	67.20%	1.20%	31.54%	0.00%	NA
VI/Aromatic	96	97.90%	1.00%	0.00%	1.04%	NA
Intermediate	90	72.20%	1.10%	17.78%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0321841885	A -> DEL	N	N	silent_mutation	Average:8.664; most accessible tissue: Callus, score: 16.424	N	N	N	N
vg0321841885	A -> G	LOC_Os03g39300.1	downstream_gene_variant ; 3908.0bp to feature; MODIFIER	silent_mutation	Average:8.664; most accessible tissue: Callus, score: 16.424	N	N	N	N
vg0321841885	A -> G	LOC_Os03g39310.1	downstream_gene_variant ; 877.0bp to feature; MODIFIER	silent_mutation	Average:8.664; most accessible tissue: Callus, score: 16.424	N	N	N	N
vg0321841885	A -> G	LOC_Os03g39300-LOC_Os03g39310	intergenic_region ; MODIFIER	silent_mutation	Average:8.664; most accessible tissue: Callus, score: 16.424	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0321841885	4.22E-07	NA	mr1531	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
vg0321841885	NA	8.69E-06	mr1136_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