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Detailed information for vg0132716122:

Variant ID: vg0132716122 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 32716122
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:


TTTGTTTATTTACGACTAGTAGTGTCAATTGGATCAACTTGATCTCATTGCTTTCATTAAAAAAACAGTATGCAACAACAAATGACATGCATGAATTAAT[C/A]
AATGCACAAGATATTAAAAGTAGGAGGAATATATCAGGCGCTGAAAATTCTTCCCTGGCCAGAATAAGTTTGCCAGATGTTTCACATTCCAGCTTAATTT

Reverse complement sequence

AAATTAAGCTGGAATGTGAAACATCTGGCAAACTTATTCTGGCCAGGGAAGAATTTTCAGCGCCTGATATATTCCTCCTACTTTTAATATCTTGTGCATT[G/T]
ATTAATTCATGCATGTCATTTGTTGTTGCATACTGTTTTTTTAATGAAAGCAATGAGATCAAGTTGATCCAATTGACACTACTAGTCGTAAATAAACAAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.20% 1.50% 0.32% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 94.30% 4.70% 0.99% 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 99.90% 0.00% 0.13% 0.00% NA
Tropical Japonica  504 83.30% 13.90% 2.78% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0132716122 C -> A LOC_Os01g56690.1 intron_variant ; MODIFIER silent_mutation Average:64.561; most accessible tissue: Zhenshan97 root, score: 89.596 N N N N