CVE-2026-31972: SAMtools is a program for reading, manipulating and writing bioinformatics file formats

Q: How do I fix CVE-2026-31972?

samtools: upgrade to 1.21.1. Exact commands for each OS are on this page.

Q: Is CVE-2026-31972 being exploited?

CVE-2026-31972 is not on the CISA Known Exploited Vulnerabilities list at the time of the last update. Check again, as this can change.

Q: What does CVE-2026-31972 affect?

CVE-2026-31972 affects samtools. Severity is critical (CVSS 9.8). 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, opt

Q: How urgent is CVE-2026-31972?

Priority 51/100. Critical severity; Remotely exploitable, no login, no user action

This month

CRITICAL 9.8REMOTEUPGRADE

CVE-2026-31972 is a critical-severity flaw (CVSS 9.8) affecting samtools. Below: why it ranks where it does, which versions are affected, what to do, and the exact commands.

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 nee

Why this priority

Critical severity
Remotely exploitable, no login, no user action

A fixed release or distro patch exists.

Risk facts

CVSS score	9.8 (Critical)
Attack vector	Network (remote)
Attack complexity	Low
Privileges needed	None
User interaction	None
EPSS exploit chance	0.5% (top 55%)
CISA exploited list	No
Weakness	CWE-416
Published	2026-03-18
Last modified	2026-06-17

Publisher (CNA): GitHub, Inc. · Vendor: samtools

Last updated 2026-06-17 · Sources: CVE Program, NVD, CISA KEV, EPSS and vendor advisories · How we score

Am I affected?

Timeline

2026-03-18 21:16 UTCPublished CVE record published
2026-06-17 10:34 UTCUpdated Record last modified

samtools samtools UPGRADE

Affected: < 1.21.1

Fixed in: 1.21.1

Safe to downgrade to: no unaffected older release

1. Check installed version

apt-cache policy samtools || rpm -q samtools || samtools --version

2. UPGRADE to 1.21.1 (Debian / Ubuntu)

sudo apt update && sudo apt install --only-upgrade samtools

2. UPGRADE (RHEL / Amazon Linux / Fedora)

sudo dnf upgrade samtools

Note

Distros often backport fixes without changing the version number. Confirm with the distro advisory or changelog.

Verify at the official source NVD · CVE Program · Report a problem with this page
Scores and fixes here are computed automatically from those and other public sources. Confirm with the vendor advisory before changing production systems.

Quick answers

How do I fix CVE-2026-31972?

samtools: upgrade to 1.21.1. Exact commands for each OS are on this page.

Is CVE-2026-31972 being exploited?

CVE-2026-31972 is not on the CISA Known Exploited Vulnerabilities list at the time of the last update. Check again, as this can change.

What does CVE-2026-31972 affect?

CVE-2026-31972 affects samtools. Severity is critical (CVSS 9.8). 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, opt

How urgent is CVE-2026-31972?

Priority 51/100. Critical severity; Remotely exploitable, no login, no user action

Related CVEs

CVE-2026-31973 HIGH 7.5 UPGRADE SAMtools is a program for reading, manipulating and writing bioinformatics file formats

References

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