Vulnerability · Published Mar 18, 2026 · Assigned by GitHub_M
CVE-2026-31972samtools mpileup has use-after-free leading to an invalid read
Medium 6.9
In plain English
A medium-severity use-after-free in samtools from samtools. There are no confirmed reports of exploitation so far. The chance it is exploited in the next 30 days is estimated at 0.5% (higher than 46% of all known vulnerabilities). Fixed versions are available - upgrade the affected package.
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.
Affected packages & fixed versions
| Ecosystem | Package | Fixed in | Advisory |
|---|---|---|---|
| Debian:12 | samtools | no fix listed | DEBIAN-CVE-2026-31972 |
| Debian:13 | samtools | no fix listed | DEBIAN-CVE-2026-31972 |
| Debian:14 | samtools | 1.24-2 | DEBIAN-CVE-2026-31972 |
| Ubuntu:22.04:LTS | samtools | no fix listed | UBUNTU-CVE-2026-31972 |
| Ubuntu:24.04:LTS | samtools | no fix listed | UBUNTU-CVE-2026-31972 |
| Ubuntu:25.10 | samtools | no fix listed | UBUNTU-CVE-2026-31972 |
| Ubuntu:26.04:LTS | samtools | no fix listed | UBUNTU-CVE-2026-31972 |
| Ubuntu:26.10 | samtools | no fix listed | UBUNTU-CVE-2026-31972 |
Affected products (as reported)
Weakness: CWE-416 · Vector: 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