amedes_simulated_se

This lineage analysis report provides an overview over all mutations found in the sample and the deconvoluted lineage abundances. The tables below display the summarized results from single-nucleotide-variant (SNV) calling and their translation into protein mutations. A bar chart visualizes the proportions of lineages that are derived by deconvolution of the set of mutations that is matching the provided list of lineage - characterizing mutations (signature mutations). For detailed method description please consult the documentation
Note: Deconvolution results are biased by the number of reads and by the number of signature mutations that were found for this sample. Check with the QC report to be able to assess how trustworthy the results are.

1 Mutation analysis

The following tables combine the results from the variant calling which are SNVs, their frequency and read coverage. They get translated to get the info about the resulting protein mutation and on which gene they are located. If the SNV matches a provided signature mutation it is marked which of the provided lineages they characterize.

Table 1: SNVs from sample matching signature mutations

Table 2: SNVs from sample not matching any signature mutations

2 Lineage analysis

Lineage proportion values are derived by deconvolution of the tracked signature mutations. Deconvolution is done by using a robust regression model. It aims to predict the individual contributions of the lineages to the observed mutation frequencies in the bulk wastewater sample. For detailed method description, please consult the documentation

The following bar plot shows the proportion of each lineage in the sample as predicted by the deconvolution model. For the case of multiple lineages being indistinguishable because of shared signature mutations, the deconvolution result for this group is distributed equally across each grouped lineage and they all get the same value.

3 Analysis Parameter

3.1 LoFreq filter

LoFreq is used with default filter settings:
minimum coverage 10
Strand-Bias Multiple Testing Correction, fdr corr. pvalue > 0.001000
Minimum SNV Quality (Phred) 63
Minimum Indel Quality (Phred) 47

3.2 VEP settings

  • Species: SARS-CoV-2
  • Assembly: ASM985889v3
Matched Annotations from NCBI and EMBL-EBI (MANE) yes
Restrict results by severity of consequence no
upstream/downstream distance 5000bp

4 Raw data

Called SNVs:
Download SNVs.csv

Variant effect prediction (Ensemble VEP output):
Download VEP_out.csv