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.

Project Subscriptions

Vendors Products
Samtools Subscribe
Samtools Subscribe
Advisories

No advisories yet.

Fixes

Solution

No solution given by the vendor.


Workaround

No workaround given by the vendor.

History

Thu, 19 Mar 2026 19:00:00 +0000

Type Values Removed Values Added
CPEs cpe:2.3:a:samtools:samtools:*:*:*:*:*:*:*:*
Metrics cvssV3_1

{'score': 9.8, 'vector': 'CVSS:3.1/AV:N/AC:L/PR:N/UI:N/S:U/C:H/I:H/A:H'}


Thu, 19 Mar 2026 15:15:00 +0000

Type Values Removed Values Added
Metrics ssvc

{'options': {'Automatable': 'yes', 'Exploitation': 'none', 'Technical Impact': 'partial'}, 'version': '2.0.3'}


Thu, 19 Mar 2026 09:45:00 +0000

Type Values Removed Values Added
First Time appeared Samtools
Samtools samtools
Vendors & Products Samtools
Samtools samtools

Thu, 19 Mar 2026 00:30:00 +0000

Type Values Removed Values Added
References

Wed, 18 Mar 2026 21:00:00 +0000

Type Values Removed Values Added
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.
Title samtools mpileup has use-after-free leading to an invalid read
Weaknesses CWE-416
References
Metrics cvssV4_0

{'score': 6.9, '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'}


Projects

Sign in to view the affected projects.

cve-icon MITRE

Status: PUBLISHED

Assigner: GitHub_M

Published:

Updated: 2026-03-19T14:22:59.713Z

Reserved: 2026-03-10T15:40:10.486Z

Link: CVE-2026-31972

cve-icon Vulnrichment

Updated: 2026-03-18T23:08:19.727Z

cve-icon NVD

Status : Analyzed

Published: 2026-03-18T21:16:26.070

Modified: 2026-03-19T18:54:51.970

Link: CVE-2026-31972

cve-icon Redhat

No data.

cve-icon OpenCVE Enrichment

Updated: 2026-03-19T08:55:34Z

Weaknesses