Examples

The following examples demonstrate sequencing results that customers can expect. These examples are not password protected and can be opened by anyone. Actual customer data will be password protected to ensure your sensitive data is secure.

Plasmid Sequencing of pUC19


Below is the example output using the famous cloning vector pUC19.
Name: pUC stands for plasmid University of California, referencing where it was developed.
Developed: In the early 1980s by Joachim Messing and colleagues at the University of California, San Francisco and Davis.



Interactive IGV link
https://igv.angstrominno.com/?sessionURL=/data/AI-1046_1_pUC19/session.json#

AB1 chromatogram files showing the sequence quality (loads in SnapGene)
pUC19.ab1

Coverage Plot (using de novo assembly as reference) 
De novo assembly (FASTA File)
pUC19.fasta

GenBank File
pUC19.gbk

Annotationed GFF File
pUC19.gff

Histogram of read lengths. Occasionally plasmid multimers will appear
Interactive Plasmid Map
pUC19_interactive_map
Click the link above to get the full interactive view. Below is a screenshot. 

Per Base Data
pUC19.tsv

Raw Data (compressed FASTQ)
pUC19.fastq.gz

Contamination Report
  • Total reads: 852
  • Raw E. coli filtered reads: 6
  • Contamination Percent: 0.70%
Multimer Analysis
  • Read Classification (by percentage, molar fraction, and mass fraction):
  • 1-mer: 40.02% (341 reads), Molar Fraction: 97.71%, Mass Fraction: 95.52%
  • 2-mer: 0.94% (8 reads), Molar Fraction: 2.29%, Mass Fraction: 4.48%
  • Total Reads (including unclassified reads): 852

BRESEQ (using published pUC19 as reference)

 

Amplicon Sequencing of SS3 locus

The SS3 locus is a commonly used integration locus in E. coli engineering (Bassalo 2016). Here we validate the wildtype locus (containing the gRNA target sequence) using primers 

 

Primer Name Sequence
SS3_forward GGC GGT GCA CAG CAA CAC G
SS3_reverse CCG GTG ATA CAG CTT CAA TTC CAA CC

This amplifies a short product about 250 bp long.

Interactive IGV View. After doing nanopore sequencing we can confirm the wildtype sequence with intact gRNA targeting region.

https://igv.angstrominno.com/?sessionURL=/data/AI-1047_1_SS3_locus/session.json#

Summary Table indicates that the first sample with SS3 no mutations compared to the reference.

Raw Reads (FASTQ file)

https://drive.google.com/file/d/1TZZRJAVHOC5lJUFUnrBPtQ9cGdO-Ykc0/view?usp=drive_link

Coverage Plot

Bacterial Genome Sequencing of BL21(DE3)

 

The example below shows the whole genome sequencing result for BL21(DE3), a host frequently used for T7 promoter expression. 

For the analysis below, the updated 2024 reference sequence NZ_CP053602.1 was used. 

Interactive IGV weblink:

https://igv.angstrominno.com/?sessionURL=/data/AI-1045_1_BL21_DE3/session.json#

Screenshot below shows a random mutation at cnoX gene

Assembly (FASTA format)

BL21_DE3.fasta

GenBank File

BL21_DE3.gbk

Screenshot below of the annotated map

BRESEQ (showing all the mutations relative to the reference)

Raw FASTQ file (typically around 200 Mb)

BL21_DE3.fastq.gz