Vulnerability · CVE-2026-31972
SAMtools is a program for reading, manipulating and writing bioinformatics file formats.
Published Mar 18, 2026 · corrected/updated Jun 17, 2026 · samtools samtools · evidence confidence high
SAMtools is a program for reading, manipulating and writing bioinformatics file formats. The 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.
Grounded briefings
Catalog interpretations for three audiences. Each brief cites ingested metadata and the original advisories below. They are not independent research and they do not invent exploit steps.
Executive
CVE-2026-31972 is a medium public vulnerability record for samtools samtools. It is not currently listed in the CISA Known Exploited catalog. Check the linked vendor or CERT advisories for patch status. This summary is a catalog interpretation of the ingested metadata and cites the original advisories below.
System administrator
Identify whether samtools samtools is in your estate, then compare installed versions with the affected ranges. Affected packages or ranges on record: samtools/samtools. Check the linked vendor or CERT advisories for patch status. Prefer the vendor or distribution advisory linked in Sources before changing production systems. This is a catalog interpretation, not a runbook.
Security analyst
Signals on file: CVSS 6.9, EPSS 0.7%. It is not currently listed in the CISA Known Exploited catalog. Weakness classes: CWE-416. Sources contributing to this record: cve_org, epss, nvd. Public exploit references, when present, are outbound links only and are not proof of active exploitation. This is a catalog interpretation of stored metadata.
Exploitation and remediation
Exploitation evidence
Not listed as known exploited in CISA KEV. Not in CISA KEV or VulnCheck KEV.
Patch and remediation
No required-action text is stored yet. Use the vendor or CERT links in Sources for patch availability.
Safe detection guidance
Compare installed versions with the affected ranges below and verify the advisory from the original publisher. This site stores metadata and outbound links only; it does not ship exploit code or proof-of-concept payloads.
Code
The project this record applies to. Exploit listings stay in References.
Timeline
Detection, updates, and resolution for this record.
Mar 18, 2026 · NIST NVD
Detected
SAMtools is a program for reading, manipulating and writing bioinformatics file formats. The 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 positi
Jun 17, 2026 · NIST NVD
Updated
SAMtools is a program for reading, manipulating and writing bioinformatics file formats. The 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 positi
Affected
- cpe samtools/samtoolsversion unspecified
Sources
- CVE.orgVulnerability recordCVE-2026-31972
Official CVE identifier
cve.org - FIRST EPSSExploitation probabilityCVE-2026-31972
30-day exploitation probability 0.7%
first.org - NIST NVDVulnerability recordCVE-2026-31972
SAMtools is a program for reading, manipulating and writing bioinformatics file formats. The 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 p
nvd.nist.gov