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Detailed information for vg0123776002:

Variant ID: vg0123776002 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 23776002
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.76, G: 0.24, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

ATTAAGAGGAGTAAAGTAATACAAGACAGACAGAGAAGAACAGGGAGGAGAGAGGAGGGGAGGAGAAAAGGAGAAACGGAAAAAGACACACTAAATCACT[G/A]
ATCTCCCAAAACTATTGTGTGACCTAGACCTAGTTGAGGTATTGCAGTCCTCGCCAATCTCCAAAGTGTGGCTTCTTCTGACATTGCCTTGGCGCCCTCA

Reverse complement sequence

TGAGGGCGCCAAGGCAATGTCAGAAGAAGCCACACTTTGGAGATTGGCGAGGACTGCAATACCTCAACTAGGTCTAGGTCACACAATAGTTTTGGGAGAT[C/T]
AGTGATTTAGTGTGTCTTTTTCCGTTTCTCCTTTTCTCCTCCCCTCCTCTCTCCTCCCTGTTCTTCTCTGTCTGTCTTGTATTACTTTACTCCTCTTAAT

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	24.20%	19.90%	0.28%	55.59%	NA
All Indica	2759	2.90%	7.80%	0.36%	89.02%	NA
All Japonica	1512	67.90%	24.30%	0.07%	7.74%	NA
Aus	269	0.40%	91.80%	0.00%	7.81%	NA
Indica I	595	3.00%	0.30%	0.84%	95.80%	NA
Indica II	465	3.70%	3.70%	0.22%	92.47%	NA
Indica III	913	0.20%	11.30%	0.00%	88.50%	NA
Indica Intermediate	786	5.30%	11.70%	0.51%	82.44%	NA
Temperate Japonica	767	93.10%	6.40%	0.00%	0.52%	NA
Tropical Japonica	504	38.30%	41.10%	0.20%	20.44%	NA
Japonica Intermediate	241	49.80%	46.10%	0.00%	4.15%	NA
VI/Aromatic	96	6.20%	92.70%	0.00%	1.04%	NA
Intermediate	90	35.60%	26.70%	2.22%	35.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0123776002	G -> A	LOC_Os01g41930.1	5_prime_UTR_variant ; 500.0bp to feature; MODIFIER	silent_mutation	Average:13.914; most accessible tissue: Callus, score: 87.572	N	N	N	N
vg0123776002	G -> A	LOC_Os01g41920.1	upstream_gene_variant ; 3319.0bp to feature; MODIFIER	silent_mutation	Average:13.914; most accessible tissue: Callus, score: 87.572	N	N	N	N
vg0123776002	G -> A	LOC_Os01g41910.1	downstream_gene_variant ; 4487.0bp to feature; MODIFIER	silent_mutation	Average:13.914; most accessible tissue: Callus, score: 87.572	N	N	N	N
vg0123776002	G -> DEL	N	N	silent_mutation	Average:13.914; most accessible tissue: Callus, score: 87.572	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0123776002	NA	1.10E-08	mr1642_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