CVE-2026-31972— samtools mpileup has use-after-free leading to an invalid read
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I. Basic Information for CVE-2026-31972
Vulnerability Information
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Vulnerability Title
samtools mpileup has use-after-free leading to an invalid read
Source: NVD (National Vulnerability Database)
Vulnerability 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.
Source: NVD (National Vulnerability Database)
CVSS Information
N/A
Source: NVD (National Vulnerability Database)
Vulnerability Type
释放后使用
Source: NVD (National Vulnerability Database)
Vulnerability Title
samtools 资源管理错误漏洞
Source: CNNVD (China National Vulnerability Database)
Vulnerability Description
samtools是samtools开源的一个处理高通量测序数据的工具集。 samtools 1.21.1之前版本和1.22之前版本存在资源管理错误漏洞，该漏洞源于mpileup命令过早丢弃数据，可能导致读取已释放内存。
Source: CNNVD (China National Vulnerability Database)
CVSS Information
N/A
Source: CNNVD (China National Vulnerability Database)
Vulnerability Type
N/A
Source: CNNVD (China National Vulnerability Database)
Affected Products
II. Public POCs for CVE-2026-31972
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- Fix mpileup -a bug (#2229) · samtools/samtools@3036eb9 · GitHubx_refsource_MISC
- https://nvd.nist.gov/vuln/detail/CVE-2026-31972
Same Patch Batch · samtools · 2026-03-18 · 12 CVEs total
| CVE-2026-31962 | HTSlib CRAM reader has heap buffer overflow due to improper validation of input | |
| CVE-2026-31964 | HTSlib CRAM decoder has a NULL Pointer Dereference | |
| CVE-2026-31963 | HTSlib CRAM reader has heap buffer overflow due to improper validation of input | |
| CVE-2026-31965 | HTSlib CRAM reader has out-of-bounds reads due to improper validation of input | |
| CVE-2026-31966 | HTSlib CRAM reader has out-of-bounds read due to improper validation of input | |
| CVE-2026-31967 | HTSlib CRAM reader has out-of-bounds read due to improper validation of input | |
| CVE-2026-31968 | HTSlib CRAM decoder vulnerable to buffer overflow | |
| CVE-2026-31971 | HTSlib CRAM decoder vulnerable to buffer overflow | |
| CVE-2026-31969 | HTSlib CRAM decoder has a heap buffer overflow | |
| CVE-2026-31970 | HTSlib BGZF index file reader has a heap buffer overflow | |
| CVE-2026-31973 | NULL pointer dereference in samtools cram-size |
IV. Related Vulnerabilities
Same vendor: samtools
- CVE-2026-31973
NULL pointer dereference in samtools cram-size - CVE-2026-31971
HTSlib CRAM decoder vulnerable to buffer overflow - CVE-2026-31970
HTSlib BGZF index file reader has a heap buffer overflow - CVE-2026-31969
HTSlib CRAM decoder has a heap buffer overflow - CVE-2026-31968
HTSlib CRAM decoder vulnerable to buffer overflow
V. Comments for CVE-2026-31972
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