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Detailed information for vg0526335948:

Variant ID: vg0526335948 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 26335948
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 327. )

Flanking Sequence (100 bp) in Reference Genome:

TAGGCAAAAGAAGTGTAGAGTCACGAACAAATAATAAAGGTCCCAGCTGAACAAGGAAAAGCGGAGCATTTTCATCGCCAGAATTTGAACCACCACGCGA[C/T]
GACTCCAACCTCCAAAGGTCCCCACGTGCAACAACTGAAGTCTCAAAGTCATGGTGCCTGGTCTCGTATGTTGCTGAGATATTTATGGTTCCCTGCATCA

Reverse complement sequence

TGATGCAGGGAACCATAAATATCTCAGCAACATACGAGACCAGGCACCATGACTTTGAGACTTCAGTTGTTGCACGTGGGGACCTTTGGAGGTTGGAGTC[G/A]
TCGCGTGGTGGTTCAAATTCTGGCGATGAAAATGCTCCGCTTTTCCTTGTTCAGCTGGGACCTTTATTATTTGTTCGTGACTCTACACTTCTTTTGCCTA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	98.80%	1.10%	0.04%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	99.70%	0.10%	0.13%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	99.70%	0.00%	0.26%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	46.90%	53.10%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0526335948	C -> T	LOC_Os05g45400.1	synonymous_variant ; p.Ser251Ser; LOW	synonymous_codon	Average:57.78; most accessible tissue: Callus, score: 79.709	N	N	N	N