Minor Variants Summary (Juliet)

Input data
Timestamp:2020-05-04T04:51:17.667Z
Input File:subsampled.mapped.bam
Command Line Call:juliet -c /home/UNIXHOME/etseng/projects2020/SARS_Cov2/LabCorp/sarscov2.json subsampled.mapped.bam subsampled.minperc10.juliet.html subsampled.minperc10.juliet.json --min-perc 10
Juliet Version:1.12.0 (commit v1.12.0*)
Target config
Config Version:1
Reference Name:NC_045512.2
Reference Length:29903
Genes:
Variant Discovery
orf1a-p1
NC_045512.2 Sample Variants
Codon AA Pos AA Codon % Coverage Affected Drugs*
A G C S 2839SA G T 100186
Pos A C G T - N
-3 0 0 0 185 1 0
-2 1 0 0 185 0 0
-1 0 0 0 186 0 0
0 186 0 0 0 0 0
1 0 0 186 0 0 0
2 0 0 0 186 0 0
3 0 186 0 0 0 0
4 186 0 0 0 0 0
5 0 0 186 0 0 0
orf1a-p2
NC_045512.2 Sample Variants
Codon AA Pos AA Codon % Coverage Affected Drugs*
C T C L 1531LC T T 10085
Pos A C G T - N
-3 0 0 86 0 1 0
-2 0 0 87 0 0 0
-1 87 0 0 0 0 0
0 0 87 0 0 0 0
1 0 0 0 87 0 0
2 0 0 0 85 2 0
3 0 0 0 87 0 0
4 0 0 0 87 0 0
5 0 0 0 87 0 0
ORF8
NC_045512.2 Sample Variants
Codon AA Pos AA Codon % Coverage Affected Drugs*
T T A L 84ST C A 10089
Pos A C G T - N
-3 0 0 0 180 0 0
-2 0 0 180 0 0 0
-1 0 0 0 180 0 0
0 0 0 0 180 0 0
1 0 89 0 0 0 0
2 89 0 0 0 0 0
3 0 89 0 0 0 0
4 0 89 0 0 0 0
5 0 0 0 88 1 0
*https://www.ncbi.nlm.nih.gov/nuccore/NC_045512 (last updated 2020-03-17)
Legend

General:

  • Every table represents a gene.
  • Positions are relative to the current gene.
  • Each row stands for a mutated amino acid.
  • Positions without significant mutations are omitted.
  • All coordinates are in reference space.
  • The mutated nucleotide is highlighted in the codon.
  • Percentage is per codon.
  • Coverage includes deletions.
  • Drugs affected by known drug resistance mutations are listed in the corresponding column.

Alignment Details:

  • Clicking on a row unfolds the counts of the multiple sequence alignment of the codon position and up to ±3 surrounding positions.
  • Nucleotides of this codon are in red and wild type in bold.

Limitations:

  • Deletions and insertions are being ignored in this version.

This software is for research only and has not been clinically validated!

Drug SummariesNo known drug-resistance mutations present.