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Fencer Vulns
critical 9.8

CVE-2026-31972 json

samtools mpileup has use-after-free leading to an invalid read

published 2026-03-18 7 mo ago modified 2026-06-17 4 mo ago also EUVD-2026-12956

cvss
9.8
version 3.1, NVD
cisa kev
Not listed
not in CISA's catalog
epss
0.5%
EPSS 0.5% chance of exploitation in 30 days, percentile 46%
public exploits
0
none known

Summary

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.

Patch / fix

  • samtools samtools 1.21.1
  • samtools Debian 14 1.22.1-1

debian advisories DEBIAN-CVE-2026-31972

Vendor advisories

What the vendors themselves say about their products: affected, fixed or not affected, and what to do.

red hat product security vex CVE-2026-31972 updated cvss 6.1

samtools: SAMtools: Information Disclosure and Denial of Service via use-after-free vulnerability in mpileup command

  • Red Hat All currently supported Red Hat products
    not affected: vulnerable code not present

Red Hat CSAF VEX © Red Hat, Inc., from https://security.access.redhat.com/data/csaf/v2/vex/; changed: reduced to product statuses and remediations. CC BY 4.0 · csaf

CISA SSVC

Exploitation
none
Automatable
yes
Technical impact
partial
Assessed
7 mo ago

Exploit prediction

0.55% chance of exploitation in the next 30 days, higher than 46% of all scored CVEs (FIRST EPSS, 2026-11-08).

CVSS scores

assigned by version score vector
CNA 4.0 6.9 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
CNA 4.0 6.9 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/E:X/CR:X/IR:X/AR:X/MAV:X/MAC:X/MAT:X/MPR:X/MUI:X/MVC:X/MVI:X/MVA:X/MSC:X/MSI:X/MSA:X/S:X/AU:X/R:X/V:X/RE:X/U:X
NVD 3.1 9.8 CVSS:3.1/AV:N/AC:L/PR:N/UI:N/S:U/C:H/I:H/A:H

Affected products

  • samtools samtools

Classification

Weakness

References

Sources

Fencer Vulns keeps one entry per vulnerability: the CVE id wins, then GHSA, and records that alias each other are merged, except that two CVEs always keep separate entries. The same data is available as JSON.