CVE catalog
CVE-2026-31972
SAMtools is a program for reading, manipulating and writing bioinformatics file formats. The `mpileup` command outputs DNA sequences that have been aligned against a known reference. On each output li
- Severity
- Medium · CVSS 6.9
- Published
- Source
- [NVD] · [CVE record]
- EPSS
- 0.54% · Oct 25, 2026
SAMtools is a program for reading, manipulating and writing bioinformatics file formats. The `mpileup` command outputs DNA sequences that have been aligned against a known reference. On each output line it writes the reference position, optionally the reference DNA base at that position (obtained from a separate file) and all of the DNA bases that aligned to that position. As the output is ordered by position, reference data that is no longer needed is discarded once it has been printed out. Under certain conditions the data could be discarded too early, leading to an attempt to read from a pointer to freed memory. This bug may allow information about program state to be leaked. It may also cause a program crash through an attempt to access invalid memory. This bug is fixed in versions 1.21.1 and 1.22. There is no workaround for this issue.
Vulnerable and fixed packages
Distribution-reported package versions and fixes. These do not depend on matching against the OpenFactory package catalog.
| Distribution | Package | Release | Version | Status |
|---|---|---|---|---|
| Debian | samtools | sid | 1.24-2 | vulnerable |
| Debian | samtools | forky | 1.24-2 | vulnerable |
| Debian | samtools | trixie | 1.21-1 | vulnerable |
| Debian | samtools | bookworm | 1.16.1-1 | vulnerable |
| Cpe | samtools | Not reported | Not reported | vulnerable |
Fixed-version evidence
| Distribution | Package | Type | Release | Fixed version | Urgency | Origin | Bugs |
|---|---|---|---|---|---|---|---|
| Debian | samtools | source | sid | (unfixed) | unimportant | Not reported | Not reported |
| Debian | samtools | source | forky | (unfixed) | unimportant | Not reported | Not reported |
| Debian | samtools | source | trixie | (unfixed) | unimportant | Not reported | Not reported |
| Debian | samtools | source | bookworm | (unfixed) | unimportant | Not reported | Not reported |
OpenFactory catalog packages
[Debian 12 (Bookworm)]
- [samtools]Affected
Details (2)
1.16.1-1· amd64 · bookwormAffected
nvd · samtools · debian · bookworm; nvd · samtools · debian · 12
1.16.1-1· arm64 · bookwormAffected
nvd · samtools · debian · bookworm; nvd · samtools · debian · 12
- [samtools-test]Affected
Source package: [samtools]
Details (2)
1.16.1-1· all · bookwormAffected
nvd · samtools · debian · bookworm; nvd · samtools · debian · 12
1.16.1-1· all · bookwormAffected
nvd · samtools · debian · bookworm; nvd · samtools · debian · 12
[Debian 13 (Trixie)]
- [samtools]Affected
Details (2)
1.21-1· amd64 · trixieAffected
nvd · samtools · debian · 13
1.21-1· arm64 · trixieAffected
nvd · samtools · debian · 13
- [samtools-test]Affected
Source package: [samtools]
Details (2)
1.21-1· all · trixieAffected
nvd · samtools · debian · 13
1.21-1· all · trixieAffected
nvd · samtools · debian · 13
Observed:
References
- [https://nvd.nist.gov/vuln/detail/CVE-2026-31972]
- [https://osv.dev/vulnerability/DEBIAN-CVE-2026-31972]
- [https://security-tracker.debian.org/tracker/CVE-2026-31972]
- [https://security.access.redhat.com/data/csaf/v2/vex/2026/cve-2026-31972.json]
[Debian Security Tracker] · [FIRST EPSS] · [National Vulnerability Database (NVD)] · [OSV Package Vulnerability Database] · [Red Hat security advisories and VEX]