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Detailed information for vg0416635232:

Variant ID: vg0416635232 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 16635232
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.52, A: 0.48, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

ATTTTCGGTGCTCTGAAAATTCTAGTAAAATTTGAGGGCTCCTTTTAGACCAAGGAGAATTTAAGAAAAATACTCTGGGCCACATTTGATTTTTTCTTGT[G/A]
CACATTTTAATAAATTCTATTGTTCCTTTTAGAGTGATTTTTAATTTGGGATGAATTTACAGGACGTGACAGGTAGGTACAATTTAGTACATAAAATTAT

Reverse complement sequence

ATAATTTTATGTACTAAATTGTACCTACCTGTCACGTCCTGTAAATTCATCCCAAATTAAAAATCACTCTAAAAGGAACAATAGAATTTATTAAAATGTG[C/T]
ACAAGAAAAAATCAAATGTGGCCCAGAGTATTTTTCTTAAATTCTCCTTGGTCTAAAAGGAGCCCTCAAATTTTACTAGAATTTTCAGAGCACCGAAAAT

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	62.20%	37.10%	0.00%	0.72%	NA
All Indica	2759	43.70%	55.20%	0.00%	1.01%	NA
All Japonica	1512	88.40%	11.30%	0.00%	0.26%	NA
Aus	269	90.30%	9.70%	0.00%	0.00%	NA
Indica I	595	46.90%	52.40%	0.00%	0.67%	NA
Indica II	465	28.00%	71.00%	0.00%	1.08%	NA
Indica III	913	54.30%	44.70%	0.00%	0.99%	NA
Indica Intermediate	786	38.40%	60.30%	0.00%	1.27%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	67.50%	31.70%	0.00%	0.79%	NA
Japonica Intermediate	241	96.30%	3.70%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	65.60%	32.20%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0416635232	G -> DEL	N	N	silent_mutation	Average:44.42; most accessible tissue: Minghui63 panicle, score: 68.46	N	N	N	N
vg0416635232	G -> A	LOC_Os04g28160.1	downstream_gene_variant ; 2149.0bp to feature; MODIFIER	silent_mutation	Average:44.42; most accessible tissue: Minghui63 panicle, score: 68.46	N	N	N	N
vg0416635232	G -> A	LOC_Os04g28170.1	downstream_gene_variant ; 4422.0bp to feature; MODIFIER	silent_mutation	Average:44.42; most accessible tissue: Minghui63 panicle, score: 68.46	N	N	N	N
vg0416635232	G -> A	LOC_Os04g28170.2	downstream_gene_variant ; 4247.0bp to feature; MODIFIER	silent_mutation	Average:44.42; most accessible tissue: Minghui63 panicle, score: 68.46	N	N	N	N
vg0416635232	G -> A	LOC_Os04g28160-LOC_Os04g28170	intergenic_region ; MODIFIER	silent_mutation	Average:44.42; most accessible tissue: Minghui63 panicle, score: 68.46	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0416635232	1.00E-05	1.12E-10	mr1552	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