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Detailed information for vg0125220764:

Variant ID: vg0125220764 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 25220764
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.81, A: 0.19, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

CCATGGTGATCAGCATGAGGCAACACCACCTACTCCACAGGCTAGCAATATATTTTATACTCACATCAATTATATGCATATGTCTTTGTCAGACCTTCCT[G/A]
ACCATTATTACTTTATCAGGTCATAGCTATAGCACAGCTAGATAAAAAACATAAATCTTCTACGGCTGATGAGAATCTTGGCCATGGAGGGTTAGTGCCA

Reverse complement sequence

TGGCACTAACCCTCCATGGCCAAGATTCTCATCAGCCGTAGAAGATTTATGTTTTTTATCTAGCTGTGCTATAGCTATGACCTGATAAAGTAATAATGGT[C/T]
AGGAAGGTCTGACAAAGACATATGCATATAATTGATGTGAGTATAAAATATATTGCTAGCCTGTGGAGTAGGTGGTGTTGCCTCATGCTGATCACCATGG

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	52.90%	46.70%	0.04%	0.36%	NA
All Indica	2759	78.50%	20.80%	0.07%	0.62%	NA
All Japonica	1512	2.00%	98.00%	0.00%	0.00%	NA
Aus	269	97.80%	2.20%	0.00%	0.00%	NA
Indica I	595	61.20%	38.00%	0.00%	0.84%	NA
Indica II	465	87.50%	12.00%	0.00%	0.43%	NA
Indica III	913	86.60%	13.10%	0.00%	0.22%	NA
Indica Intermediate	786	76.80%	21.90%	0.25%	1.02%	NA
Temperate Japonica	767	0.30%	99.70%	0.00%	0.00%	NA
Tropical Japonica	504	1.80%	98.20%	0.00%	0.00%	NA
Japonica Intermediate	241	7.90%	92.10%	0.00%	0.00%	NA
VI/Aromatic	96	8.30%	91.70%	0.00%	0.00%	NA
Intermediate	90	37.80%	62.20%	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
vg0125220764	G -> A	LOC_Os01g44010.1	downstream_gene_variant ; 1905.0bp to feature; MODIFIER	silent_mutation	Average:28.297; most accessible tissue: Callus, score: 56.652	N	N	N	N
vg0125220764	G -> A	LOC_Os01g44030.1	downstream_gene_variant ; 1637.0bp to feature; MODIFIER	silent_mutation	Average:28.297; most accessible tissue: Callus, score: 56.652	N	N	N	N
vg0125220764	G -> A	LOC_Os01g44020.1	intron_variant ; MODIFIER	silent_mutation	Average:28.297; most accessible tissue: Callus, score: 56.652	N	N	N	N
vg0125220764	G -> DEL	N	N	silent_mutation	Average:28.297; most accessible tissue: Callus, score: 56.652	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0125220764	NA	5.28E-08	mr1222	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
vg0125220764	NA	4.80E-17	mr1146_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