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Detailed information for vg0416255837:

Variant ID: vg0416255837 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 16255837
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAAATCCCACCCCTATATATATGTCTTCTTCCTCCTCCAGCTGTCCGAGCAAGCTTCAAAATTTCTTCAAAAAAGAGGGGAGGTCATGCTAAAATTTCTA[A/G]
TGAATTTATTTTGGTGATTACATACAAATCGGAGGTGCCTAAAAGGTTTGCAACTTCATCCTCCAATGTTTTTTTTGTCATATTACATTTGCATCTATAT

Reverse complement sequence

ATATAGATGCAAATGTAATATGACAAAAAAAACATTGGAGGATGAAGTTGCAAACCTTTTAGGCACCTCCGATTTGTATGTAATCACCAAAATAAATTCA[T/C]
TAGAAATTTTAGCATGACCTCCCCTCTTTTTTGAAGAAATTTTGAAGCTTGCTCGGACAGCTGGAGGAGGAAGAAGACATATATATAGGGGTGGGATTTT

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	76.30%	0.20%	6.77%	16.69%	NA
All Indica	2759	84.60%	0.10%	7.10%	8.19%	NA
All Japonica	1512	66.50%	0.10%	1.12%	32.28%	NA
Aus	269	61.30%	0.00%	18.59%	20.07%	NA
Indica I	595	91.10%	0.00%	8.57%	0.34%	NA
Indica II	465	91.00%	0.00%	5.59%	3.44%	NA
Indica III	913	74.30%	0.00%	8.87%	16.87%	NA
Indica Intermediate	786	88.00%	0.30%	4.83%	6.87%	NA
Temperate Japonica	767	72.40%	0.00%	0.52%	27.12%	NA
Tropical Japonica	504	51.00%	0.00%	1.98%	47.02%	NA
Japonica Intermediate	241	80.50%	0.40%	1.24%	17.84%	NA
VI/Aromatic	96	35.40%	4.20%	51.04%	9.38%	NA
Intermediate	90	75.60%	2.20%	8.89%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0416255837	A -> DEL	N	N	silent_mutation	Average:23.04; most accessible tissue: Minghui63 young leaf, score: 33.985	N	N	N	N
vg0416255837	A -> G	LOC_Os04g27500.1	upstream_gene_variant ; 731.0bp to feature; MODIFIER	silent_mutation	Average:23.04; most accessible tissue: Minghui63 young leaf, score: 33.985	N	N	N	N
vg0416255837	A -> G	LOC_Os04g27490.1	downstream_gene_variant ; 3402.0bp to feature; MODIFIER	silent_mutation	Average:23.04; most accessible tissue: Minghui63 young leaf, score: 33.985	N	N	N	N
vg0416255837	A -> G	LOC_Os04g27490-LOC_Os04g27500	intergenic_region ; MODIFIER	silent_mutation	Average:23.04; most accessible tissue: Minghui63 young leaf, score: 33.985	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0416255837	NA	7.66E-08	mr1544_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
vg0416255837	8.64E-06	4.72E-07	mr1952_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