Use After Free in Samtools
CVE-2026-31972
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.
Vulnerability class: Use-After-Free
EPSS: 0.005 (41.0th percentile) — read the EPSS interpretation.
CVSS v3 metric
CVSS v3 base score 9.8 (Critical). Vector: CVSS:3.1/AV:N/AC:L/PR:N/UI:N/S:U/C:H/I:H/A:H.
Affected products
- Samtools — versions < 1.21.1
Weakness classification (CWE)
References
- security-advisories@github.com (x_refsource_CONFIRM, Vendor Advisory)
- security-advisories@github.com (Patch, x_refsource_MISC)
- af854a3a-2127-422b-91ae-364da2661108 (Mailing List, Third Party Advisory)
Frequently asked questions
- What is CVE-2026-31972?
- CVE-2026-31972 is a critical-severity vulnerability in Samtools, classified under Use After Free. CVSS score: 9.8/10. Published 2026-03-18.
- How severe is CVE-2026-31972?
- Critical severity. CVSS v3 base score is 9.8 out of 10.