CVE-2019-10269: BWA (aka Burrow-Wheeler Aligner) before 2019-01-23 has a stack-based buffer overflow in the bns_restore functi

Q: How do I fix CVE-2019-10269?

burrow-wheeler aligner: upgrade to 2019-01-23; ubuntu linux: mitigate or apply the listed mitigation. Exact commands for each OS are on this page.

Q: Is CVE-2019-10269 being exploited?

CVE-2019-10269 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-2019-10269 affect?

CVE-2019-10269 affects burrow-wheeler aligner, ubuntu linux. Severity is critical (CVSS 9.8). BWA (aka Burrow-Wheeler Aligner) before 2019-01-23 has a stack-based buffer overflow in the bns_restore function in bntseq.c via a long sequence name in a .alt file.

Q: How urgent is CVE-2019-10269?

Priority 71/100. Critical severity; Public exploit reference; Remotely exploitable, no login, no user action; On your watchlist

This week

CRITICAL 9.8REMOTEWATCHLISTUPGRADEMITIGATE

CVE-2019-10269 is a critical-severity flaw (CVSS 9.8) affecting burrow-wheeler aligner, ubuntu linux. Below: why it ranks where it does, which versions are affected, what to do, and the exact commands.

BWA (aka Burrow-Wheeler Aligner) before 2019-01-23 has a stack-based buffer overflow in the bns_restore function in bntseq.c via a long sequence name in a .alt file.

Why this priority

Critical severity
Public exploit reference
Remotely exploitable, no login, no user action
On your watchlist

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	2.9% (top 13%)
CISA exploited list	No
Weakness	CWE-787
Published	2019-03-29
Last modified	2026-06-17

Publisher (CNA): MITRE · Vendor: burrow-wheeler aligner project · canonical

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

Am I affected?

Timeline

2019-03-29 05:29 UTCPublished CVE record published
2026-06-17 02:10 UTCUpdated Record last modified

burrow-wheeler aligner project burrow-wheeler aligner UPGRADE

Affected: < 2019-01-23

Fixed in: 2019-01-23

Safe to downgrade to: no unaffected older release

1. Check installed version

apt-cache policy burrow-wheeler-aligner || rpm -q burrow-wheeler-aligner || burrow-wheeler-aligner --version

2. UPGRADE to 2019-01-23 (Debian / Ubuntu)

sudo apt update && sudo apt install --only-upgrade burrow-wheeler-aligner

2. UPGRADE (RHEL / Amazon Linux / Fedora)

sudo dnf upgrade burrow-wheeler-aligner

Note

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

canonical ubuntu linux MITIGATE

Affected: 18.04 · 19.04

Fixed in: no fixed release known

Safe to downgrade to: a release before 18.04

Check your OS release

cat /etc/os-release; uname -r

Debian / Ubuntu

sudo apt update && sudo apt full-upgrade

RHEL / Amazon Linux / Fedora

sudo dnf upgrade --refresh

Windows

Install the latest cumulative update from Windows Update

If no patch exists yet

OS downgrades are not safe. Apply the vendor mitigation from the advisory and restrict exposure.

Exact fixes by distribution

A distro patch exists: prefer upgrading over downgrading.

Fedora 46 · nodejs-pnpm12 · FIXED · 12.17.0-1.fc46 · FEDORA-2026-7adfb2bcdd · source

sudo dnf upgrade --advisory=FEDORA-2026-7adfb2bcdd

Fedora ELN · wget2 · FIXED · 2.3.0-3.eln159 · FEDORA-2026-811b4922a5 · source

sudo dnf upgrade --advisory=FEDORA-2026-811b4922a5

Ubuntu 22.04 · bwa · NOT AFFECTED

Ubuntu 20.04 · bwa · NOT AFFECTED

Debian 12 · bwa · FIXED · 0.7.17-3

sudo apt update && sudo apt install --only-upgrade bwa dpkg --compare-versions "$(dpkg-query -W -f='${Version}' bwa)" ge "0.7.17-3" && echo PATCHED || echo STILL-VULNERABLE

Debian 13 · bwa · FIXED · 0.7.17-3

sudo apt update && sudo apt install --only-upgrade bwa dpkg --compare-versions "$(dpkg-query -W -f='${Version}' bwa)" ge "0.7.17-3" && echo PATCHED || echo STILL-VULNERABLE

Public exploits and detection

Public code exists for this CVE. Treat unpatched systems as at risk, and only run PoCs in a lab.

Write-up: coreymhudson.github.io/bwa_vulnerabilties/

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-2019-10269?

burrow-wheeler aligner: upgrade to 2019-01-23; ubuntu linux: mitigate or apply the listed mitigation. Exact commands for each OS are on this page.

Is CVE-2019-10269 being exploited?

CVE-2019-10269 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-2019-10269 affect?

CVE-2019-10269 affects burrow-wheeler aligner, ubuntu linux. Severity is critical (CVSS 9.8). BWA (aka Burrow-Wheeler Aligner) before 2019-01-23 has a stack-based buffer overflow in the bns_restore function in bntseq.c via a long sequence name in a .alt file.

How urgent is CVE-2019-10269?

Priority 71/100. Critical severity; Public exploit reference; Remotely exploitable, no login, no user action; On your watchlist

Software pages

Ubuntu vulnerabilities

Related CVEs

CVE-2019-11371 CRITICAL 9.8 DOWNGRADE BWA (aka Burrow-Wheeler Aligner) 0.7.17 r1198 has a Buffer Overflow via a long prefix that is mishandled in bn

References

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