Vulnerability 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.
CVSS Score
CRITICAL
Affected Products
| Vendor | Product | Versions |
|---|---|---|
| Samtools | Samtools | < 1.21.1 |
Related Weaknesses (CWE)
References
- https://github.com/samtools/samtools/commit/3036eb9af945fcef359427a2d359855553daPatch
- https://github.com/samtools/samtools/security/advisories/GHSA-72c8-4jf3-f27pVendor Advisory
- http://www.openwall.com/lists/oss-security/2026/03/18/11Mailing ListThird Party Advisory
FAQ
What is CVE-2026-31972?
CVE-2026-31972 is a vulnerability with a CVSS score of 9.8 (CRITICAL). 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...
How severe is CVE-2026-31972?
CVE-2026-31972 has been rated CRITICAL with a CVSS base score of 9.8/10. This is considered a critical vulnerability requiring immediate attention.
Is there a patch for CVE-2026-31972?
Check the references section above for vendor advisories and patch information. Affected products include: Samtools Samtools.