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Detailed information for vg0419029854:

Variant ID: vg0419029854 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 19029854
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 322. )

Flanking Sequence (100 bp) in Reference Genome:

TTCGTTCCTAAGCATAATAGCATCAAGTAACATTTCATTATATTTTGCAAATCATGTTTATGGAAGCCTAATAATGAATTTACCTAATAGCTCAATTGAT[A/G]
CGCATGAGTTTGTCTGAGTCGTATTTGTATAATATATTCAACTTAGAATAGTTGAACTATAGGCGATTGTAAGCAAGGTAGGGATGTCCTCATTTATAGG

Reverse complement sequence

CCTATAAATGAGGACATCCCTACCTTGCTTACAATCGCCTATAGTTCAACTATTCTAAGTTGAATATATTATACAAATACGACTCAGACAAACTCATGCG[T/C]
ATCAATTGAGCTATTAGGTAAATTCATTATTAGGCTTCCATAAACATGATTTGCAAAATATAATGAAATGTTACTTGATGCTATTATGCTTAGGAACGAA

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	93.40%	3.10%	3.43%	0.00%	NA
All Indica	2759	97.20%	0.70%	2.10%	0.00%	NA
All Japonica	1512	84.90%	8.50%	6.55%	0.00%	NA
Aus	269	99.30%	0.00%	0.74%	0.00%	NA
Indica I	595	94.30%	0.50%	5.21%	0.00%	NA
Indica II	465	95.70%	2.80%	1.51%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	97.20%	0.30%	2.54%	0.00%	NA
Temperate Japonica	767	76.00%	16.00%	7.95%	0.00%	NA
Tropical Japonica	504	96.40%	0.20%	3.37%	0.00%	NA
Japonica Intermediate	241	89.20%	2.10%	8.71%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	1.10%	3.33%	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
vg0419029854	A -> G	LOC_Os04g31790.1	intron_variant ; MODIFIER	silent_mutation	Average:37.464; most accessible tissue: Zhenshan97 young leaf, score: 61.386	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0419029854	1.33E-06	1.54E-08	mr1588_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