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Detailed information for vg0219891676:

Variant ID: vg0219891676 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 19891676
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTGTTGCAAGAAGGAACGAGCATTTCATTTCAGCCTCGTTGTTTATCAGTCACTAGTAAAAGAAGATCAGTACGCGTTTAAATAATTTACTAGCTAAACC[G/A]
TGAATTTGTGAAGAGCATTACTGAAATATAAAGGCCCTATTTGGTATAGCTCCAAGTCCTATATCCACGCTGAATTTGGAGTTTCTAAGTTAAATTATAA

Reverse complement sequence

TTATAATTTAACTTAGAAACTCCAAATTCAGCGTGGATATAGGACTTGGAGCTATACCAAATAGGGCCTTTATATTTCAGTAATGCTCTTCACAAATTCA[C/T]
GGTTTAGCTAGTAAATTATTTAAACGCGTACTGATCTTCTTTTACTAGTGACTGATAAACAACGAGGCTGAAATGAAATGCTCGTTCCTTCTTGCAACAA

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	98.40%	0.90%	0.70%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	95.20%	2.70%	2.12%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	91.10%	5.00%	3.91%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	97.90%	1.20%	0.83%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	100.00%	0.00%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0219891676	G -> A	LOC_Os02g33460.1	upstream_gene_variant ; 3634.0bp to feature; MODIFIER	silent_mutation	Average:49.297; most accessible tissue: Callus, score: 80.38	N	N	N	N
vg0219891676	G -> A	LOC_Os02g33450-LOC_Os02g33460	intergenic_region ; MODIFIER	silent_mutation	Average:49.297; most accessible tissue: Callus, score: 80.38	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0219891676	8.38E-06	8.38E-06	mr1038	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
vg0219891676	NA	3.97E-08	mr1038_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
vg0219891676	8.96E-09	8.96E-09	mr1389_2	Jap_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