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docs: fix escaping
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@ivan-aksamentov
ivan-aksamentov committed Jul 4, 2024
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Showing 1 changed file with 7 additions and 7 deletions.
14 changes: 7 additions & 7 deletions docs/user/output-files/04-results-tsv.md
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Expand Up @@ -25,7 +25,7 @@ Every row in tabular output corresponds to 1 input sequence. The meaning of colu
| seqName | Name of the sequence (as provided in the input file) | string | hCoV-19/USA/SEARCH-4652-SAN/2020 |
| clade | Assigned clade | string | 20A |
| qc.overallScore | Overall [quality control](../algorithm/07-quality-control) score | float | 23.5 |
| qc.overallStatus | Overall [quality control](../algorithm/07-quality-control) status | string: `good\|mediocre\|bad` | mediocre |
| qc.overallStatus | Overall [quality control](../algorithm/07-quality-control) status | string: `good | mediocre |bad` | mediocre |
| totalSubstitutions | Total number of detected nucleotide substitutions | non-negative integer | 2 |
| totalDeletions | Total number of deleted nucleotide bases | non-negative integer | 15 |
| totalInsertions | Total number of inserted nucleotide bases | non-negative integer | 3 |
Expand Down Expand Up @@ -75,31 +75,31 @@ Every row in tabular output corresponds to 1 input sequence. The meaning of colu
| relativeMutations\['<search.name\>'\].aaDeletions | List of detected aminoacid deletions relative to the node of interest | comma separated list of strings | N:E31-,N:E32- |
| qc.missingData.missingDataThreshold | Threshold that was used for "Missing data" QC rule | int | 3000 |
| qc.missingData.score | Score for "Missing data" QC rule | float | 0.5 |
| qc.missingData.status | Status for "Missing data" QC rule | string: `good\|mediocre\|bad` | mediocre |
| qc.missingData.status | Status for "Missing data" QC rule | string: `good | mediocre |bad` | mediocre |
| qc.missingData.totalMissing | Total number of missing nucleotides used in "Missing data" QC rule | non-negative integer | 238 |
| qc.mixedSites.mixedSitesThreshold | Threshold used for "Mixed sites" QC rule | int | 10 |
| qc.mixedSites.score | Score for "Mixed sites" QC rule | float | 0.5 |
| qc.mixedSites.status | Status for "Mixed sites" QC rule | string: `good\|mediocre\|bad` | good |
| qc.mixedSites.status | Status for "Mixed sites" QC rule | string: `good | mediocre |bad` | good |
| qc.mixedSites.totalMixedSites | Total number of ambiguous nucleotides used for "Mixed sites" QC rule | non-negative integer | 2 |
| qc.privateMutations.cutoff | Cutoff parameter used for "Private mutations" QC rule | int | 3 |
| qc.privateMutations.excess | Excess parameter used for "Private mutations" QC rule | int | 1 |
| qc.privateMutations.score | Score for "Private mutations" QC rule | float | 0.5 |
| qc.privateMutations.status | Status for "Private mutations" QC rule | string: `good\|mediocre\|bad` | good |
| qc.privateMutations.status | Status for "Private mutations" QC rule | string: `good | mediocre |bad` | good |
| qc.privateMutations.total | Weighted sum of private mutations used for "Private mutations" QC rule | non-negative integer | 4 |
| qc.snpClusters.clusteredSNPs | Clustered SNP detected for "SNP clusters" QC rule | comma separated list of strings | C241T,C2061T |
| qc.snpClusters.score | Score for "SNP clusters" QC rule | float | 0.5 |
| qc.snpClusters.status | Status for "SNP clusters" QC rule | string: `good\|mediocre\|bad` | bad |
| qc.snpClusters.status | Status for "SNP clusters" QC rule | string: `good | mediocre |bad` | bad |
| qc.snpClusters.totalSNPs | Total number of SNPs for "SNP clusters" QC rule | non-negative integer | 2 |
| qc.frameShifts.frameShifts | List of detected frame shifts in "Frame shifts" QC rule (excluding ignored) | comma separated list of strings | N:33-420 |
| qc.frameShifts.totalFrameShifts | Total number of detected frame shifts in for "Frame shifts" QC rule (excluding ignored) | non-negative integer | 1 |
| qc.frameShifts.frameShiftsIgnored | List of frame shifts detected, but ignored due to ignore list | comma separated list of strings | ORF8:109-111 |
| qc.frameShifts.totalFrameShiftsIgnored | Total number of frame shifts detected, but ignored due to ignore list | non-negative integer | 1 |
| qc.frameShifts.score | Score for "Frame shifts" QC rule | float | 0.5 |
| qc.frameShifts.status | Status for "Frame shifts" QC rule | string: `good\|mediocre\|bad` | bad |
| qc.frameShifts.status | Status for "Frame shifts" QC rule | string: `good | mediocre |bad` | bad |
| qc.stopCodons.stopCodons | List of detected stop codons in "Stop codons" QC rule | comma separated list of strings | ORF1a:4715,ORF1a:4716 |
| qc.stopCodons.totalStopCodons | Total number of detected stop codons in "Stop codons" QC rule | non-negative integer | 2 |
| qc.stopCodons.score | Score for "Stop codons" QC rule | float | 0.5 |
| qc.stopCodons.status | Status for "Stop codons" QC rule | string: `good\|mediocre\|bad` | bad |
| qc.stopCodons.status | Status for "Stop codons" QC rule | string: `good | mediocre |bad` | bad |
| isReverseComplement | Whether query sequences were transformed using reverse complement operation before alignment | boolean | false |
| errors | List of errors during processing | comma separated list of strings | |
| warnings | List of warnings during processing | comma separated list of strings | |
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