Critical
samtools — security advisory
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.
- Products
- samtools
- Affected versions
- 0.1.19-1, 0.1.19-1ubuntu1, 1.10-3, 1.13-2, 1.13-4, 1.17-1, 1.18-1, 1.19-1, 1.19.2-1, 1.19.2-1build1, 1.19.2-1build2, 1.21-1, 1.22.1-1, 1.4.1-1build1, 1.5-1build1, 1.6-3ubuntu1, 1.6-4, 1.7-1, 1.9-4, 1.9-5, 1.9-6, 1.9-7
- Fixed versions
- Not specified
- CVEs
- CVE-2026-31972
- Confirmed fixed CVEs
- Not specified
- Updated in this feed
- 31 Oct 2026, 02:43 UTC · Revision 1
Source evidence
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.
osv:UBUNTU-CVE-2026-31972
samtools
Fixed versions: Not specified
samtools
Fixed versions: Not specified
samtools
Fixed versions: Not specified
samtools
Fixed versions: Not specified
samtools
Fixed versions: Not specified
samtools
Fixed versions: Not specified
samtools
Fixed versions: Not specified
samtools
Fixed versions: Not specified
samtools
Fixed versions: Not specified
Complete source record
{
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"modified": "2026-10-17T12:58:50.997566590Z",
"provider": "osv",
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"https://www.cve.org/CVERecord?id=CVE-2026-31972",
"https://github.com/samtools/samtools/security/advisories/GHSA-72c8-4jf3-f27p",
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"source_id": "core-osv",
"document_id": 359108,
"published_at": "2026-03-18T21:16:00+00:00"
}