Description
Decode a pileup read-start mapping-quality symbol.
Sequence text, ambiguity codes and encoded quality scores describe different information. Literal alphabets and Phred transformations can be checked without identifying a molecule or proving calibrated sequencing accuracy; missingness and reporting encodings require explicit conventions.
Decode a pileup read-start mapping-quality symbol.
When to use this tool
Use Pileup Readstart Quality Symbol when checking the stated sequence token, ambiguity, quality symbol or local trimming convention.
How to use the tool and how it works
- Enter token. Use the units and conventions below.
- Run the tool. Correct any format, range, or cross-field input error before interpreting the output.
- Read mappingQuality. Use the output convention below.
Decode a pileup read-start mapping-quality symbol. Require two UTF-16 units beginning with caret and second character code 33..126; mappingQuality = code-33.1
Pileup read-start notation includes a mapping-quality character encoded with ASCII offset 33; the marker is only one part of a pileup record.2
| Input field | Meaning and units | Accepted input |
|---|---|---|
| token | Token | Required. Text; maximum UTF-16 length 8192. |
| Output field | Interpretation | Returned shape |
|---|---|---|
| mappingQuality | Mapping Quality | Required. Safe integer. |
{
"input": {
"token": "^I"
},
"output": {
"mappingQuality": 40
}
}Limitations and assumptions
- Only this two-character marker is decoded; the following base, complete pileup line and underlying read mapping are not checked.
- Inputs must satisfy both the field types and the cross-field conditions above. Invalid input causes an error; a successful false flag or documented placeholder is a different result.
Alternative or Complementary methods
Use a complete format-aware sequence/quality workflow and the appropriate reference/genetic code; assess biological identity and quality calibration independently.
References
-
Calculation and input contract: bioinformatics/pileup-readstart-quality-symbol — tool.io
-
samtools mpileup: pileup format — SAMtools maintainers
Similar or alternative tools
- FASTQ Quality Trimming One End Budget
Trim a consecutive low-quality run from one supplied end.
- Bioinformatics: Fastq Quality Char Phred Score
Decode one FASTQ quality character under a supplied offset.