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Detailed information for vg0138753428:

Variant ID: vg0138753428 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 38753428
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

GGCTTGTGTGCCATTTGTGTGGTTCCGGGAAATATAGTGTGTTTTACTCTTGGTAGTTCTAGTGAATTGACAATGGTGTGATGTAACTAGTTTTTGGCTA[G/T]
GGAAAAGTGAAGTGCTTCTATTTCATAGTTTTCGTACTGAATGGAAAATATTTAGTTACATACTGATATATGAATCTGCTCCCCCCGTTTCCTATCATAA

Reverse complement sequence

TTATGATAGGAAACGGGGGGAGCAGATTCATATATCAGTATGTAACTAAATATTTTCCATTCAGTACGAAAACTATGAAATAGAAGCACTTCACTTTTCC[C/A]
TAGCCAAAAACTAGTTACATCACACCATTGTCAATTCACTAGAACTACCAAGAGTAAAACACACTATATTTCCCGGAACCACACAAATGGCACACAAGCC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	79.80%	19.70%	0.08%	0.44%	NA
All Indica	2759	66.00%	33.10%	0.14%	0.76%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	97.40%	2.60%	0.00%	0.00%	NA
Indica I	595	46.20%	52.90%	0.00%	0.84%	NA
Indica II	465	97.20%	2.60%	0.00%	0.22%	NA
Indica III	913	56.70%	42.30%	0.22%	0.77%	NA
Indica Intermediate	786	73.30%	25.40%	0.25%	1.02%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	10.00%	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
vg0138753428	G -> T	LOC_Os01g66710.1	downstream_gene_variant ; 2660.0bp to feature; MODIFIER	silent_mutation	Average:38.669; most accessible tissue: Callus, score: 72.221	N	N	N	N
vg0138753428	G -> T	LOC_Os01g66730.1	downstream_gene_variant ; 1630.0bp to feature; MODIFIER	silent_mutation	Average:38.669; most accessible tissue: Callus, score: 72.221	N	N	N	N
vg0138753428	G -> T	LOC_Os01g66730.2	downstream_gene_variant ; 1658.0bp to feature; MODIFIER	silent_mutation	Average:38.669; most accessible tissue: Callus, score: 72.221	N	N	N	N
vg0138753428	G -> T	LOC_Os01g66720.1	intron_variant ; MODIFIER	silent_mutation	Average:38.669; most accessible tissue: Callus, score: 72.221	N	N	N	N
vg0138753428	G -> DEL	N	N	silent_mutation	Average:38.669; most accessible tissue: Callus, score: 72.221	N	N	N	N