CVE-2026-31972
samtools mpileup has use-after-free leading to an invalid read
- Published
- Updated
- Reserved
- Assigned by
- GitHub_M
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.
Scores
| Scored by | CVSS | Score | Vector |
|---|---|---|---|
| GitHub_MCNA (assigner) | 4.0 | Medium6.9 | CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:N/VC:L/VI:N/VA:L/SC:N/SI:N/SA:N |
| NVDNVD · Analyzed | 4.0 | Medium6.9 | CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:N/VC:L/VI:N/VA:L/SC:N/SI:N/SA:N/E:X/CR:X/IR:X/AR:X/MAV:X/MAC:X/MAT:X/MPR:X/MUI:X/MVC:X/MVI:X/MVA:X/MSC:X/MSI:X/MSA:X/S:X/AU:X/R:X/V:X/RE:X/U:X |
- EPSS (exploitation in 30 days)
- 0.55% · top 54% of all CVEs (6 Nov 2026)
- CISA SSVC
- Exploitation: none · Automatable: yes · Technical impact: partial
The list uses the assigner's score when there is one, then CISA's, then NVD's: Medium 6.9.
Weakness
Affected products
References (3)
- https://github.com/samtools/samtools/security/advisories/GHSA-72c8-4jf3-f27p (opens in a new tab)x_refsource_CONFIRM
- https://github.com/samtools/samtools/commit/3036eb9af945fcef359427a2d359855553da4adf (opens in a new tab)x_refsource_MISC
- http://www.openwall.com/lists/oss-security/2026/03/18/11 (opens in a new tab)
Sources
The same CVE in the primary databases and aggregators, to check against.
- CVE.org record (opens in a new tab)
- CVE List JSON (GitHub) (opens in a new tab)
- NVD (opens in a new tab)
- FIRST EPSS (opens in a new tab)
- OSV.dev (opens in a new tab)
- GitHub Advisories (opens in a new tab)
- CIRCL Vulnerability-Lookup (opens in a new tab)
Badge for a README or a ticket
[](https://trackcve.app/cve/CVE-2026-31972)Record last updated .