N.B. The versions of pangolin and nextclade are indicated in the footer of this report. Because of the fast moving nature of the pandemic these versions may not be the most recent, but we check daily for new versions. More details are provided here.
This section displays basic QC metrics indicating read data quality.
The panel below lists samples which failed to produce results from the primary ARTIC analysis. Samples not listed here were analysed successfully, but may still contain inconclusive or invalid results. See the following sections for further indications of failed or inconclusive results.
All samples analysed successfully
Plots below indicate depth of coverage from data used within the Artic analysis coloured by amplicon pool. Variant filtering during the ARTIC analysis mandates a minimum coverage of at least 20X at variant/genotyping loci for a call to be made.
NB: To better display all possible data, the depth axes of the plots below are not tied between plots for different samples. Care should be taken in comparing depth across samples.
The following tables and figures are derived from
the output of bcftools stats.
Variant counts:
| sample | MNPs | SNPs | indels | multiallelic SNP sites | multiallelic sites | no-ALTs | others | records |
|---|---|---|---|---|---|---|---|---|
| SAMN23469685.pass.named.stats | 2 | 47 | 5 | 0 | 0 | 0 | 0 | 54 |
| SAMN23469691.pass.named.stats | 2 | 33 | 3 | 0 | 0 | 0 | 0 | 38 |
| negative.pass.named.stats | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
Transitions and tranversions:
| sample | ts | tv | ts/tv | ts (1st ALT) | tv (1st ALT) | ts/tv (1st ALT) |
|---|---|---|---|---|---|---|
| SAMN23469685.pass.named.stats | 30 | 17 | 1.76 | 30 | 17 | 1.76 |
| SAMN23469691.pass.named.stats | 24 | 9 | 2.67 | 24 | 9 | 2.67 |
| negative.pass.named.stats | 0 | 0 | 0.00 | 0 | 0 | 0.00 |
Substitution types
Base substitutions aggregated across all samples (symmetrised by pairing)
Indel lengths
Insertion and deletion lengths aggregated across all samples.
The following view is produced by the nextclade software.
The table shows errors, warnings or failed genes per sample:
| Sample Name | errors | warnings | failed genes |
|---|---|---|---|
| SAMN23469685 MN908947.3 | None | None | None |
| SAMN23469691 MN908947.3 | None | None | None |
| negative MN908947.3 | None | None | None |
Note: For targeted sequencing, such as SpikeSeq, Nextclade may report 'Missing data' QC fails. This is expected and not a concern provided the regions of interest are not reported as missing.
The table below reports the lineage of each sample as calculated by pangolin.
| taxon | lineage | conflict | ambiguity_score | scorpio_call | scorpio_support | scorpio_conflict | scorpio_notes | version | pangolin_version | scorpio_version | constellation_version | is_designated | qc_status | qc_notes | note |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SAMN23469685 MN908947.3 | BA.1.19 | 0.0 | NaN | Omicron (BA.1-like) | 0.83 | 0.0 | scorpio call: Alt alleles 48; Ref alleles 0; Amb alleles 7; Oth alleles 3 | PUSHER-v1.21 | 4.3 | 0.3.17 | v0.1.12 | False | pass | Ambiguous_content:0.16 | Usher placements: BA.1.19(1/1) |
| SAMN23469691 MN908947.3 | BA.1 | 0.0 | NaN | Probable Omicron (Unassigned) | 0.66 | 0.0 | scorpio call: Alt alleles 21; Ref alleles 0; Amb alleles 11; Oth alleles 0 | PUSHER-v1.21 | 4.3 | 0.3.17 | v0.1.12 | False | pass | Ambiguous_content:0.28 | Usher placements: BA.1(4/4); scorpio found insufficient support to assign a specific lineage |
| negative MN908947.3 | Unassigned | NaN | NaN | NaN | NaN | NaN | NaN | PUSHER-v1.21 | 4.3 | 0.3.17 | v0.1.12 | False | fail | Ambiguous_content:0.9 | NaN |
The table below highlights versions of key software used within the analysis.
| Name | Version |
|---|---|
| medaka | 1.7.2 |
| minimap2 | 2.18-r1015 |
| bcftools | 1.16 |
| samtools | 1.16.1 |
| artic | 1.3.0 |
| pangolin | 4.3 |
| pangolin-data | 1.21 |
| constellations | v0.1.12 |
| scorpio | 0.3.17 |
| nextclade_data_tag | 2023-06-16T12:00:00Z |
The table below highlights values of the main parameters used in this analysis.
| Key | Value |
|---|---|
| help | False |
| version | False |
| out_dir | output |
| artic_threads | 4 |
| pangolin_threads | 4 |
| analyse_unclassified | False |
| fastq | ont_wf_artic |
| sample | None |
| sample_sheet | ont_samplesheet_wf-artic.csv |
| normalise | 200 |
| report_depth | 100 |
| basecaller_cfg | dna_r9.4.1_450bps_hac |
| medaka_variant_model | None |
| scheme_name | SARS-CoV-2 |
| scheme_version | ARTIC/V3 |
| list_schemes | False |
| custom_scheme | None |
| genotype_variants | None |
| report_clade | True |
| report_lineage | True |
| report_coverage | True |
| report_variant_summary | True |
| pangolin_version | 4.2 |
| nextclade_version | 2.11.0 |
| nextclade_data_tag | None |
| update_data | False |
| aws_image_prefix | None |
| aws_queue | None |
| disable_ping | False |
| lab_id | None |
| testkit | None |
| process_label | artic |
| monochrome_logs | False |
| validate_params | True |
| show_hidden_params | False |
| schema_ignore_params | show_hidden_params,validate_params,monochrome_logs,aws_queue,aws_image_prefix,pangolin_version,nextclade_version,wf,process_label |
| wf | {'example_cmd': ['--fastq wf-artic-demo/fastq', '--sample_sheet wf-artic-demo/sample_sheet.csv', '--scheme_name SARS-CoV-2', '--scheme_version Midnight-ONT/V3'], 'container_sha': 'shaa5485f2d1c9085c23b266273556a4ce01e5e0dd9', 'nextclade_sha': 'shaede3ca9a1b17c2a1d0696ef7ff8503ec167d5df9', 'pangolin_sha': 'sha1266e6040bf6e9f02e569f0eba5011a17d47f7aa'} |
| _min_len | 400 |
| _max_len | 700 |
| _scheme_version | ARTIC/V3 |
| _scheme_name | SARS-CoV-2 |
| _max_softclip_length | 0 |
| _pangolin_options |
This report was produced using the
epi2me-labs/wf-artic. The
workflow can be run using nextflow epi2me-labs/wf-artic --help
Version details Revision: master Git Commit: 98641c5bd7e14004608647086a3ebe0b73cd8822
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