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Detailed information for vg0132054027:

Variant ID: vg0132054027 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 32054027
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:


TTTTTGTTGTAGAACGCGCTCCTTTCACCTTTTTGGAACATCAATGCTCATAGCATTGTCTATATTACTCAAGGTCATGCCGGGTTCAAGTTGTCAACAA[C/T]
AATGGAAAGACAGTGTTTGATGGAGAGGTTCGTCCTGGGCAGCTGCTAATTATACCACAACACCATGTAGTTGTGAAAAAAGCACAAAGAGAAGGATGCT

Reverse complement sequence

AGCATCCTTCTCTTTGTGCTTTTTTCACAACTACATGGTGTTGTGGTATAATTAGCAGCTGCCCAGGACGAACCTCTCCATCAAACACTGTCTTTCCATT[G/A]
TTGTTGACAACTTGAACCCGGCATGACCTTGAGTAATATAGACAATGCTATGAGCATTGATGTTCCAAAAAGGTGAAAGGAGCGCGTTCTACAACAAAAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.00% 1.00% 0.00% 0.00% NA
All Indica  2759 99.60% 0.40% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 86.20% 13.80% 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 98.70% 1.30% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 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  96 100.00% 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
vg0132054027 C -> T LOC_Os01g55630.1 missense_variant ; p.Thr168Ile; MODERATE nonsynonymous_codon ; T168I Average:43.701; most accessible tissue: Callus, score: 84.144 unknown unknown TOLERATED 0.49