PCR Signature Erosion Tool (PSET) Analysis
Noblis, Inc.
January 24, 2020
Coverage
| identifier | type | PT | TP | TN | PF | FP | FN |
|---|---|---|---|---|---|---|---|
| 2019-nCoV-noblis_1 | Probe | 22 | 3 | 415 | NA | NA | NA |
| 2019-nCoV-noblis_2 | Probe | 25 | NA | 691 | NA | NA | NA |
| 2019-nCoV-noblis_3 | Probe | 25 | NA | 656 | NA | NA | NA |
| 2019-nCoV-noblis_4 | Probe | 25 | NA | 356 | NA | 3 | NA |
| ncov_e_gene | Probe | 25 | NA | 75 | 353 | 15 | NA |
| ncov_n_gene | Probe | 25 | NA | 73 | NA | 339 | NA |
| ncov_rdrp_1 | Probe | NA | 25 | 169 | 433 | 85 | NA |
| ncov_rdrp_2 | Probe | NA | 25 | 586 | 1 | 61 | NA |
The confusion matrix indicates the outcome of each assay alignment to each subject sequence. The PT and PF categories represent true positives and false positives with 100% identity. The calculation accounts for intended taxonomic target and evaluates the percentage similarity for each assay component separately. This report is based on a percentage similarity threshold of greater than or equal to 90%.
Heatmap
The heatmap represents the average alignment percentage similarity of each assay component to a subject. The y-axis sorts each subject accession by taxonomic identifier. To avoid clutter, the figure hides the subject accession.
Alignments
The alignment figure aggregates mismatches of assay amplicons to the top subject alignments comprising the PT, TP, and FN categories. The counts indicate mismatch type: transition (trs), transversion (trv), dissimilar (dis), insertion (ins), and deletion (del). The gray boxes indicate the component regions of the assays.
Metadata
## ./src/pset.py nncov.tsv nt env_nt gss epi -drivername sqlite -database data/tax/tax.db -conf-blastn task=blastn## Database: Nucleotide collection (nt)
## 57,030,965 sequences; 257,768,224,489 total bases
##
## Date: Oct 27, 2019 6:48 PM Longest sequence: 99,791,824 bases
##
## BLASTDB Version: 4
##
## Database: environmental samples
## 124,601,035 sequences; 134,952,479,671 total bases
##
## Date: Dec 10, 2019 5:25 AM Longest sequence: 40,002,466 bases
##
## BLASTDB Version: 4
##
## Database: Genome Survey Sequence, includes single-pass genomic data, exon-trapped sequences, and Alu PCR sequences.
## 40,638,741 sequences; 26,313,188,574 total bases
##
## Date: Dec 9, 2019 7:00 PM Longest sequence: 72,873 bases
##
## BLASTDB Version: 4
##
## Database: epi
## 26 sequences; 747,047 total bases
##
## Date: Jan 24, 2020 1:13 PM Longest sequence: 29,903 bases
##
## BLASTDB Version: 4