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Detailed information for vg0119654822:

Variant ID: vg0119654822 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 19654822
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:

GCTTCCGTTCCAGAACTTCTCATGATTCATATCTTCGGAGTCAACCTCATACAAGTCACCACTTCATGTCATGCGTCAACACTAGCTTGTCATTACTAGG[A/G]
TACCATGCTTGTCATTTGCTTCTAACTCGCCACCAACTGCCTCATATTAGCTTTCCTGGTCTCCGGGTGATAGCTACTTCTGCTATTTGATGCAAGGGTC

Reverse complement sequence

GACCCTTGCATCAAATAGCAGAAGTAGCTATCACCCGGAGACCAGGAAAGCTAATATGAGGCAGTTGGTGGCGAGTTAGAAGCAAATGACAAGCATGGTA[T/C]
CCTAGTAATGACAAGCTAGTGTTGACGCATGACATGAAGTGGTGACTTGTATGAGGTTGACTCCGAAGATATGAATCATGAGAAGTTCTGGAACGGAAGC

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	72.70%	0.40%	1.63%	25.24%	NA
All Indica	2759	55.60%	0.70%	1.92%	41.79%	NA
All Japonica	1512	98.10%	0.10%	0.20%	1.52%	NA
Aus	269	88.80%	0.40%	7.43%	3.35%	NA
Indica I	595	45.00%	0.20%	2.35%	52.44%	NA
Indica II	465	76.80%	0.00%	1.08%	22.15%	NA
Indica III	913	46.30%	0.80%	2.08%	50.82%	NA
Indica Intermediate	786	62.00%	1.30%	1.91%	34.86%	NA
Temperate Japonica	767	99.70%	0.00%	0.13%	0.13%	NA
Tropical Japonica	504	98.40%	0.40%	0.20%	0.99%	NA
Japonica Intermediate	241	92.50%	0.00%	0.41%	7.05%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	91.10%	0.00%	1.11%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0119654822	A -> G	LOC_Os01g35504.1	upstream_gene_variant ; 3858.0bp to feature; MODIFIER	silent_mutation	Average:23.923; most accessible tissue: Minghui63 young leaf, score: 49.581	N	N	N	N
vg0119654822	A -> G	LOC_Os01g35530.1	downstream_gene_variant ; 1651.0bp to feature; MODIFIER	silent_mutation	Average:23.923; most accessible tissue: Minghui63 young leaf, score: 49.581	N	N	N	N
vg0119654822	A -> G	LOC_Os01g35520.1	intron_variant ; MODIFIER	silent_mutation	Average:23.923; most accessible tissue: Minghui63 young leaf, score: 49.581	N	N	N	N
vg0119654822	A -> DEL	N	N	silent_mutation	Average:23.923; most accessible tissue: Minghui63 young leaf, score: 49.581	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0119654822	NA	7.92E-06	mr1963	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