Critical severity · published Mar 18, 2026
CVE-2026-31972
samtools mpileup has use-after-free leading to an invalid read
9.8
CVSS
0.5%
EPSS
No
On KEV
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 vector
CVSS:3.1/AV:N/AC:L/PR:N/UI:N/S:U/C:H/I:H/A:H
Attack vector
Network
Complexity
Low
Privileges
None
User interaction
None
Confidentiality
High
Integrity
High
Availability
High
Scope
Unchanged
Exploitation
Is it being used?
Exploit prediction (EPSS)0.5% · higher than 45% of CVEs
Exploited in the wildNo evidence yet
CISA KEVNot listed
Ransomware campaign useNot known
Affected products
Which versions
SA
samtools · samtools
< 1.21.1 · source: vendor, NVD