---
name: "last-map-probs"
section: "1"
platform: "linux"
package: "last-align"
version: "1609-1+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/last-map-probs"
---

# last-map-probs(1)

Add extra column with mapping probabilities

## NAME

last-map-probs - Add extra column with mapping probabilities

## SYNOPSIS

**last-map-probs** \[options\] lastal-alignments

## DESCRIPTION

Calculate a mismap probability for each alignment.  This is the probability that the alignment does not reflect the origin of the query sequence, assuming that one reported alignment does reflect the origin of each query.

## OPTIONS

- **-h**, **--help**

  show this help message and exit

- **-m** M, **--mismap**=*M*

  don't write alignments with mismap probability \> M (default: 0.01)

- **-s** S, **--score**=*S*

  don't write alignments with score \< S (default: e+t\*ln\[1000\])