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Fix math in readme
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jch-13 committed Sep 26, 2024
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4 changes: 2 additions & 2 deletions Readme.md
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Expand Up @@ -184,9 +184,9 @@ refers to the number of position an alignment maps to.
- Unique (best alignment maps to one position): $1$
- Pseudo-unique (best alignment maps to one position, but, with worse score, also to
others): $\frac{\text{AS}_\text{best}}{\text{AS}_\text{best} + \sum{\text{AS}_\text{subopt} |\text{subopt_alignment}|}}$
others): $\frac{\text{AS}_\text{best}}{\text{AS}_\text{best} + \sum{\text{AS}_\text{subopt} |\text{subopt}|}}$
- Non-unique (best alignment maps to multiple
positions): $\frac{1}{|\text{best_alignment}|}$
positions): $\frac{1}{|\text{best}|}$
Mapping quality is defined as the PHRED-scaled probability that an alignment is incorrect. Hence the above probabilities
are PHRED-scaled, and, for better compatibility with `BWA`, confined to the interval
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