Minor Variants Summary (Juliet)

Input data
Timestamp:2020-05-03T23:09:44.5Z
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 991733
Pos A C G T - N
-3 0 0 0 1731 2 0
-2 0 0 0 1733 0 0
-1 1 0 0 1732 0 0
0 1733 0 0 0 0 0
1 0 0 1733 0 0 0
2 0 2 0 1731 0 0
3 0 1733 0 0 0 0
4 1733 0 0 0 0 0
5 0 1 1732 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 100949
Pos A C G T - N
-3 0 0 953 0 2 0
-2 0 0 955 0 0 0
-1 955 0 0 0 0 0
0 0 955 0 0 0 0
1 0 0 0 955 0 0
2 0 0 0 949 6 0
3 0 0 0 955 0 0
4 0 0 0 955 0 0
5 0 0 0 955 0 0
Membrane
NC_045512.2 Sample Variants
Codon AA Pos AA Codon % Coverage Affected Drugs*
A C T T 7IA T T 11981
Pos A C G T - N
-3 0 0 987 0 1 0
-2 0 0 988 0 0 0
-1 0 0 0 988 0 0
0 988 0 0 0 0 0
1 0 867 0 115 6 0
2 0 0 0 987 1 0
3 987 0 0 0 1 0
4 0 0 0 988 0 0
5 0 0 0 988 0 0
ORF8
NC_045512.2 Sample Variants
Codon AA Pos AA Codon % Coverage Affected Drugs*
T T A L 84ST C A 99891
Pos A C G T - N
-3 0 0 0 1876 0 0
-2 0 0 1876 0 0 0
-1 0 0 0 1876 0 0
0 0 0 0 1876 0 0
1 1 889 0 1 0 0
2 891 0 0 0 0 0
3 0 891 0 0 0 0
4 0 891 0 0 0 0
5 0 1 0 889 1 0
Nucleocapsid
NC_045512.2 Sample Variants
Codon AA Pos AA Codon % Coverage Affected Drugs*
T C A S 194TA C A 19890
Pos A C G T - N
-3 890 0 0 0 0 0
-2 0 0 890 0 0 0
-1 0 0 0 890 0 0
0 174 0 0 716 0 0
1 0 890 0 0 0 0
2 890 0 0 0 0 0
3 890 0 0 0 0 0
4 0 0 890 0 0 0
5 890 0 0 0 0 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.