samtools: Use After Free
CVE-2026-31972 is a critical-severity use after free vulnerability in samtools, with a CVSS 3.1 base score of 9.8 out of 10. It can be exploited remotely over the network by an unauthenticated attacker, without any action from a user. Affected samtools versions: < 1.21.1. The record does not name a fixed version, so check the vendor advisory. There is no confirmed exploitation so far. EPSS estimates a 0.58% chance of exploitation within 30 days, which is low compared with other CVEs.
Critical severity: a successful attack would have severe impact.
What to do
- Check which version of samtools you run against the affected versions below, and install the vendor's latest release.
- Read the advisory on github.com for workarounds and exact fixed builds.
- Until you can update, restrict network access to the affected service so it is not reachable from untrusted networks.
Affected products and versions
Version data comes from the organisation that assigned the CVE. Confirm against the vendor advisory before deciding you are unaffected.
How the severity score breaks down
- Attack vector
- NetworkCan be exploited remotely over a network, including the internet.
- Attack complexity
- LowNo special conditions are needed; the attack works reliably.
- Privileges required
- NoneNo account or login is needed.
- User interaction
- NoneNo action by a victim is required.
- Scope
- UnchangedImpact stays within the vulnerable component.
- Confidentiality
- HighAll data handled by the component can be read.
- Integrity
- HighData or code can be modified at will.
- Availability
- HighThe component can be taken down completely.
Vector: CVSS:3.1/AV:N/AC:L/PR:N/UI:N/S:U/C:H/I:H/A:H. Scored by NVD.
| Scoring system | Score | Severity | Scored by |
|---|---|---|---|
| CVSS 4.0 | 6.9 | Medium | CNA (github.com) |
| CVSS 3.1 | 9.8 | Critical | NVD |
Official description
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.
Source: the CVE record as published by its numbering authority, via NVD and CVE.org.
The underlying weakness: Use After Free
The product reuses or references memory after it has been freed. At some point afterward, the memory may be allocated again and saved in another pointer, while the original pointer references a location somewhere within the new allocation. Any operations using the original pointer are no longer valid because the memory belongs to the code that operates on the new pointer.
How developers prevent this class of flaw
- Choose a language that provides automatic memory management.
- When freeing pointers, be sure to set them to NULL once they are freed. However, the utilization of multiple or complex data structures may lower the usefulness of this strategy.
Timeline
- CVE record published.
- CISA published its SSVC assessment (exploitation: none, automatable: yes, technical impact: partial).
- Record last changed materially (score, affected products, status or references).
References
Patches and release notes
Third-party and government advisories
- openwall.com/lists/oss-security/2026/03/18/11Mailing List, Third Party Advisory
Other vulnerabilities in samtools
- 7.5 High severity
Recent Use After Free vulnerabilities
- 7.8 High severity
- 7.8 High severity
- 8.8 High severity
- 7.5 High severity
- 8.8 High severity
- 7.5 High severity
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