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Detailed information for vg0427462098:

Variant ID: vg0427462098 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 27462098
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, G: 0.00, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:

ACGACAAATTTGTGGGTTGGTAACCAGCTTGAACGGATTAACCAGAACAGACTTTTGAAACTGTGACTGTCCATATCAAATATTGACCAACATCAGATCC[G/A]
TATTATCCAAAAGTTGTTGGCAACAAAAAAAATGCCTAAATTGTTTACTGTAAGAGACAACCACTATCTTTGTGAGTCTTTCTCTATGTGGCCAATTGAG

Reverse complement sequence

CTCAATTGGCCACATAGAGAAAGACTCACAAAGATAGTGGTTGTCTCTTACAGTAAACAATTTAGGCATTTTTTTTGTTGCCAACAACTTTTGGATAATA[C/T]
GGATCTGATGTTGGTCAATATTTGATATGGACAGTCACAGTTTCAAAAGTCTGTTCTGGTTAATCCGTTCAAGCTGGTTACCAACCCACAAATTTGTCGT

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	53.40%	46.30%	0.00%	0.38%	NA
All Indica	2759	80.80%	18.70%	0.00%	0.54%	NA
All Japonica	1512	0.50%	99.30%	0.00%	0.13%	NA
Aus	269	91.10%	8.90%	0.00%	0.00%	NA
Indica I	595	80.80%	18.70%	0.00%	0.50%	NA
Indica II	465	92.50%	7.10%	0.00%	0.43%	NA
Indica III	913	75.60%	23.90%	0.00%	0.55%	NA
Indica Intermediate	786	79.80%	19.60%	0.00%	0.64%	NA
Temperate Japonica	767	0.50%	99.50%	0.00%	0.00%	NA
Tropical Japonica	504	0.40%	99.40%	0.00%	0.20%	NA
Japonica Intermediate	241	0.80%	98.80%	0.00%	0.41%	NA
VI/Aromatic	96	5.20%	94.80%	0.00%	0.00%	NA
Intermediate	90	40.00%	58.90%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0427462098	G -> DEL	N	N	silent_mutation	Average:54.948; most accessible tissue: Minghui63 flower, score: 80.968	N	N	N	N
vg0427462098	G -> A	LOC_Os04g46310.1	downstream_gene_variant ; 2824.0bp to feature; MODIFIER	silent_mutation	Average:54.948; most accessible tissue: Minghui63 flower, score: 80.968	N	N	N	N
vg0427462098	G -> A	LOC_Os04g46330.1	downstream_gene_variant ; 4523.0bp to feature; MODIFIER	silent_mutation	Average:54.948; most accessible tissue: Minghui63 flower, score: 80.968	N	N	N	N
vg0427462098	G -> A	LOC_Os04g46310.2	downstream_gene_variant ; 2011.0bp to feature; MODIFIER	silent_mutation	Average:54.948; most accessible tissue: Minghui63 flower, score: 80.968	N	N	N	N
vg0427462098	G -> A	LOC_Os04g46320.1	intron_variant ; MODIFIER	silent_mutation	Average:54.948; most accessible tissue: Minghui63 flower, score: 80.968	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0427462098	NA	8.81E-19	mr1336_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
vg0427462098	NA	1.86E-15	mr1579_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