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Detailed information for vg0416689969:

Variant ID: vg0416689969 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 16689969
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:

TCTCTCTCAAGCCAAGTATATTCAGGATCTTTTGGATAGGGCTTCTCTCACTGATCAACGCACAGTTGAAACTCCCATGGAGCTTAATCTTCATCTTTCT[G/A]
CCACTGATGGTGAACCGTTAGCTGATCCCACTCGCTATCGTCATATTGTAGGGAGTCTTGTTTATCTTGGTGTCACTCGTCCTGATATTTCATACTCTGT

Reverse complement sequence

ACAGAGTATGAAATATCAGGACGAGTGACACCAAGATAAACAAGACTCCCTACAATATGACGATAGCGAGTGGGATCAGCTAACGGTTCACCATCAGTGG[C/T]
AGAAAGATGAAGATTAAGCTCCATGGGAGTTTCAACTGTGCGTTGATCAGTGAGAGAAGCCCTATCCAAAAGATCCTGAATATACTTGGCTTGAGAGAGA

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	96.90%	0.40%	0.34%	2.31%	NA
All Indica	2759	98.30%	0.70%	0.36%	0.69%	NA
All Japonica	1512	93.80%	0.00%	0.20%	5.95%	NA
Aus	269	98.90%	0.40%	0.74%	0.00%	NA
Indica I	595	98.20%	0.30%	0.17%	1.34%	NA
Indica II	465	97.60%	1.30%	0.43%	0.65%	NA
Indica III	913	99.50%	0.40%	0.11%	0.00%	NA
Indica Intermediate	786	97.30%	0.90%	0.76%	1.02%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	82.10%	0.00%	0.60%	17.26%	NA
Japonica Intermediate	241	98.80%	0.00%	0.00%	1.24%	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
vg0416689969	G -> DEL	N	N	silent_mutation	Average:26.494; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N
vg0416689969	G -> A	LOC_Os04g28234.1	downstream_gene_variant ; 1473.0bp to feature; MODIFIER	silent_mutation	Average:26.494; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N
vg0416689969	G -> A	LOC_Os04g28250.1	downstream_gene_variant ; 4023.0bp to feature; MODIFIER	silent_mutation	Average:26.494; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N
vg0416689969	G -> A	LOC_Os04g28234.2	intron_variant ; MODIFIER	silent_mutation	Average:26.494; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N
vg0416689969	G -> A	LOC_Os04g28234.3	intron_variant ; MODIFIER	silent_mutation	Average:26.494; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0416689969	NA	7.81E-06	mr1449_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
vg0416689969	6.44E-07	6.44E-07	mr1673_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
vg0416689969	4.90E-06	4.89E-06	mr1869_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
vg0416689969	5.72E-06	8.08E-08	mr1905_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