ISO/IEC 23092-1:2025

International
Standard
ISO/IEC 23092-1
Third edition
Information technology — Genomic
2025-01
information representation —
Part 1:
Transport and storage of genomic
information
Technologie de l'information — Représentation des informations
génomiques —
Partie 1: Transport et stockage des informations génomiques
Reference number
© ISO/IEC 2025
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© ISO/IEC 2025 – All rights reserved
ii
Contents Page
Foreword .v
Introduction .vii
1 Scope . 1
2 Normative references . 1
3 Terms and definitions . 1
4 Conventions . 4
4.1 Operators and functions .4
4.1.1 Arithmetic operators .4
4.1.2 Logical operators .4
4.1.3 Relational operators .4
4.1.4 Bitwise operators .4
4.1.5 Assignment operators .5
4.1.6 String/Character functions and operator .5
4.1.7 Data structure function and operator .5
4.1.8 Mathematical functions .5
4.1.9 Array operation functions .5
4.2 Syntax and semantics .6
4.2.1 Method of specifying syntax in tabular form .6
4.2.2 Bit ordering .6
4.2.3 Specification of syntax functions .6
4.2.4 Processes .7
5 Structure of coded genomic data . 7
5.1 Genomic sequencing data record .7
5.2 Genomic annotation data records .8
5.3 Data classes .9
5.4 Access units .10
5.5 Datasets .10
5.6 Annotation data tile .11
5.7 Annotation tables .11
5.8 Annotation access units .11
5.9 Selective access . 12
6 Data format .12
6.1 Format structure . 12
6.1.1 General . 12
6.1.2 Box order .17
6.2 Syntax for representation .18
6.3 Output data unit .19
6.4 Data structures common to file format and transport format . 20
6.4.1 File header . 20
6.4.2 Dataset group . 20
6.4.3 Dataset . 29
6.4.4 Access unit . 40
6.4.5 Block . 46
6.4.6 Annotation Table .47
6.4.7 Attribute Group .57
6.4.8 Annotation access unit .59
6.4.9 AAU block . 63
6.5 Data structures specific to file format . 64
6.5.1 General . 64
6.5.2 Indexing . 64
6.5.3 Descriptor stream .74
6.5.4 Offset .76
6.6 Data structures specific to transport format . 77

© ISO/IEC 2025 – All rights reserved
iii
6.6.1 General . 77
6.6.2 Data streams . 77
6.6.3 Dataset mapping table list . 77
6.6.4 Dataset mapping table . 78
6.6.5 Packet . 80
6.7 Reference procedures to convert transport format to file format . 81
6.7.1 Procedure for genomic sequencing data . 81
6.7.2 Procedure for genomic annotation data. 83
7 String indexing technologies .87
7.1 Master string index . 87
7.1.1 General . 87
7.1.2 Syntax . . 87
7.1.3 Master String Index Header . 87
7.1.4 String index . 88
7.1.5 Compressed string index . 90
7.2 Decoding and querying processes . 96
7.2.1 String index payload. 96
7.2.2 Helper functions . 97
7.2.3 Substring decoding process . 98
7.2.4 Suffix array lookup process . 99
7.2.5 Inverse suffix array process. 99
7.2.6 Character decoding process . 100
7.2.7 LF-mapping process . 101
7.2.8 Extended LF-mapping process . 101
7.2.9 Substring position search process . 102
7.2.10 Searching for substring positions with the string index . 103
7.2.11 Decoding a subset of the string index . 104
7.2.12 Decoding all the strings of a specific annotation data tile . 104
7.2.13 Retrieving whole strings with the string index. 106
7.2.14 Retrieving data tile index(es) associated with a position and record indexes . 107
8 Indexing for numeric range searches .110
8.1 B-Tree indexing .110
8.1.1 General .110
8.1.2 Syntax .110
8.1.3 Semantics . 111
Annex A (informative) IETF RFC 3986 specification summary .112
Annex B (informative) Selective access strategies for genomic sequencing data .113
Annex C (informative) Selective access strategies for genomic annotation data .116
Annex D (informative) Depacketization process .132
Annex E (informative) Efficient handling of symmetric annotation data .135
Bibliography .137

© ISO/IEC 2025 – All rights reserved
iv
Foreword
ISO (the International Organization for Standardization) and IEC (the International Electrotechnical
Commission) form the specialized system for worldwide standardization. National bodies that are
members of ISO or IEC participate in the development of International Standards through technical
committees established by the respective organization to deal with particular fields of technical activity.
ISO and IEC technical committees collaborate in fields of mutual interest. Other international organizations,
governmental and non-governmental, in liaison with ISO and IEC, also take part in the work.
The procedures used to develop this document and those intended for its further maintenance are described
in the ISO/IEC Directives, Part 1. In particular, the different approval criteria needed for the different types
of document should be noted. This document was drafted in accordance with the editorial rules of the ISO/
IEC Directives, Part 2 (see www.iso.org/directives or www.iec.ch/members_experts/refdocs).
ISO and IEC draw attention to the possibility that the implementation of this document may involve the
use of (a) patent(s). ISO and IEC take no position concerning the evidence, validity or applicability of any
claimed patent rights in respect thereof. As of the date of publication of this document, ISO and IEC had
received notice of (a) patent(s) which may be required to implement this document. However, implementers
are cautioned that this may not represent the latest information, which may be obtained from the patent
database available at www.iso.org/patents and https://patents.iec.ch. ISO and IEC shall not be held
responsible for identifying any or all such patent rights.
Any trade name used in this document is information given for the convenience of users and does not
constitute an endorsement.
For an explanation of the voluntary nature of standards, the meaning of ISO specific terms and expressions
related to conformity assessment, as well as information about ISO's adherence to the World Trade
Organization (WTO) principles in the Technical Barriers to Trade (TBT) see www.iso.org/iso/foreword.html.
In the IEC, see www.iec.ch/understanding-standards.
This document was prepared by Joint Technical Committee ISO/IEC JTC 1, Information technology,
Subcommittee SC 29, Coding of audio, picture, multimedia and hypermedia information.
This third edition cancels and replaces the second edition (ISO/IEC 23092-1:2020), which has been
technically revised.
The main changes are as follows:
— Updates to the overall hierarchy of data structures and box order in subclause 6.1
— Extensions for the transport and storage of genomic annotation data, in addition to genomic sequencing
data, in support of ISO/IEC 23092-6:2023 specifications while maintaining backward compatibility,
which include:
— An overview of genomic annotation data records in subclause 5.2, with detailed formats specified
in Part 6
— Basic annotation table information in dataset header (as specified in subclause 6.4.3.2) and
annotation encoding parameters in dataset parameter set (as specified in subclause 6.4.3.7)
— Additional data structures such as annotation table (atcn, as specified in subclause 6.4.6),
attribute group (agcn, as specified in subclause 6.4.7), annotation access unit (aauc, as specified
in subclause 6.4.8), AAU block (as specified in subclause 6.4.9), attribute data byte offset (adbo, as
specified in subclause 6.5.2.3) and annotation table index (atix, as specified in subclause 6.5.2.4)
— The reference procedure for conversion from transport format to file format for genomic annotation
data in subclause 6.7.2
© ISO/IEC 2025 – All rights reserved
v
— Data structure for B-Tree indexing (as specified in subclause 8.1) and selective access strategies for
genomic annotation data (as specified in Annex C)
— Extensions in support of ISO/IEC 23092-3:2022 which include:
— New container boxes for metrics metadata: DT_metrics (dtmt, as specified in subclause 6.4.3.4) and
AU_metrics (aumt, as specified in subclause 6.4.4.5), containing statistical information (with detailed
formats specified in Part 3), which allows for fast and direct extraction of statistics associated with
the dataset and access unit content
— New container boxes for clinical data linkage (CDL) metadata: DG_CDL (dgcd, as specified in
subclause 6.4.2.7), DT_CDL (dtcd, as specified in subclause 6.4.3.5) and AT_CDL (atcd, as specified
in subclause 6.4.6.4), for establishing linkages to external data sources, which enables access to the
clinical data of individual samples
— The inclusion of FM-Index-based entropy coding algorithm (as specified in Clause 7), which provides
string search capabilities in the compressed domain
A list of all parts in the ISO/IEC 23092 series can be found on the ISO and IEC websites.
Any feedback or questions on this document should be directed to the user’s national standards
body. A complete listing of these bodies can be found at www.iso.org/members.html and
www.iec.ch/national-committees.

© ISO/IEC 2025 – All rights reserved
vi
Introduction
The advent of high-throughput sequencing (HTS) technologies has the potential to boost the adoption of
genomic information in everyday practice, ranging from biological research to personalized genomic
medicine in clinics. As a consequence, the volume of generated data has increased dramatically during the
last few years, and an even more pronounced growth is expected in the near future.
At the moment, genomic information is mostly exchanged through a variety of data formats, such as
FASTA/FASTQ for unaligned sequencing reads and SAM/BAM/CRAM for aligned reads. With respect to
such formats, the ISO/IEC 23092 series provides a new solution for the representation and compression of
genome sequencing information by:
— Specifying an abstract representation of the sequencing data rather than a specific format with its direct
implementation.
— Being designed at a time point when technologies and use cases are more mature. This permits addressing
one limitation of the textual SAM format, for which the incremental ad-hoc addition of features followed
along the years, resulting in an overall redundant and suboptimal format which was unnecessarily
complicated.
— Separating free-field user-defined information with no clear semantics from the genomic data
representation. This allows a fully interoperable and automatic exchange of information between
different data producers.
— Allowing multiplexing of relevant metadata information with the data since data and metadata are
partitioned at different conceptual levels.
— Following a strict and supervised development process which has proven successful in the last 30 years
in the domain of digital media for the transport format, the file format, the compressed representation
and the application program interfaces.
The ISO/IEC 23092 series provides the enabling technology that will allow the community to create an ecosystem
of novel, interoperable, solutions in the field of genomic information processing. In particular it offers:
— Consistent, general and properly designed format definitions and data structures to store sequencing and
alignment information. A robust framework which can be used as a foundation to implement different
compression algorithms.
— Speed and flexibility in the selective access to coded data, by means of newly-designed data clustering
and optimized storage methodologies.
— Low latency in data transmission and consequent fast availability at remote locations, based on
transmission protocols inspired by real-time application domains.
— Built-in privacy and protection of sensitive information, thanks to a flexible framework which allows
customizable, secured access at all layers of the data hierarchy.
— Reliability of the technology and interoperability among tools and systems, owing to the provision of a
procedure to assess conformance to this document on an exhaustive dataset.
— Support to the implementation of a complete ecosystem of compliant devices and applications, through
the availability of a normative reference implementation covering the totality of the ISO/IEC 23092 series.
The fundamental structure of the ISO/IEC 23092 series data representation is the genomic record. The
genomic record is a data structure consisting of either a single sequence read, or a paired sequence read, and
its associated sequencing and alignment information; it may contain detailed mapping and alignment data, a
single or paired read identifier (read name) and quality values.
Without breaking traditional approaches, the genomic record introduced in the ISO/IEC 23092 series
provides a more compact, simpler and manageable data structure grouping all the information related to a
single DNA template, from simple sequencing data to sophisticated alignment information.

© ISO/IEC 2025 – All rights reserved
vii
The genomic record, although it is an appropriate logic data structure for interaction and manipulation of
coded information, is not a suitable atomic data structure for compression. To achieve high compression
ratios, it is necessary to group genomic records into clusters and to transform the information of the same
type into sets of descriptors structured into homogeneous blocks. Furthermore, when dealing with selective
data access, the genomic record is a too small unit to allow effective and fast information retrieval.
For these reasons, this document introduces the concept of access unit, which is the fundamental structure
for coding and access to information in the compressed domain.
The access unit is the smallest data structure that can be decoded by a decoder compliant with
ISO/IEC 23092-2. An access unit is composed of one block for each descriptor used to represent the
information of its genomic records; therefore, a block payload is the coded representation of all the data of
the same type (i.e. a descriptor) in a cluster.
In addition to clusters of genomic records compressed into access units, reads are further classified in six
data classes: five classes are defined according to the result of their alignment against one or more reference
sequences; the sixth class contains either reads that could not be mapped or raw sequencing data. The
classification of sequence reads into classes enables the development of powerful selective data access. In
fact, access units inherit a specific data characterization (e.g. perfect matches in Class P, substitutions in
Class M, indels in Class I, half-mapped reads in Class HM) from the genomic records composing them, and
thus constitute a data structure capable of providing powerful filtering capability for the efficient support of
many different use cases.
Access units are the fundamental, finest grain data structure in terms of content protection and in terms
of metadata association. In other words, each access unit can be protected individually and independently.
Figure 1 shows how access units, blocks and genomic records relate to each other in the ISO/IEC 23092
series data structure.
Figure 1 — Access units, blocks and genomic records

© ISO/IEC 2025 – All rights reserved
viii
Figure 2 — High-level data structure: datasets and dataset group
A dataset is a coded data structure containing headers and one or more access units. Typical datasets
could, for example, contain the complete sequencing of an individual, or a portion of it. Other datasets could
contain, for example, a reference genome or a subset of its chromosomes. Datasets are grouped in dataset
groups, as shown in Figure 2.
A simplified diagram of the dataset decoding process is shown in Figure 3.
Figure 3 — Decoding process
This document defines the syntax and semantics of the data formats for both transport and storage of
genomic information. According to this document, the compressed sequencing data can be multiplexed into
a bitstream suitable for packetization for real-time transport over typical network protocols. In storage use
cases, coded data can be encapsulated into a file format with the possibility to organize blocks per descriptor
stream or per access units, to further optimize the selective access performance to the type of data access
required by the different application scenarios. This document further provides a reference process to
convert a transport stream into a file format and vice versa.

© ISO/IEC 2025 – All rights reserved
ix
International Standard ISO/IEC 23092-1:2025(en)
Information technology — Genomic information
representation —
Part 1:
Transport and storage of genomic information
1 Scope
This document specifies data formats for both transport and storage of genomic information, including the
conversion process.
2 Normative references
The following documents are referred to in the text in such a way that some or all of their content constitutes
requirements of this document. For dated references, only the edition cited applies. For undated references,
the latest edition of the referenced document (including any amendments) applies.
ISO/IEC 10646, Information technology — Universal coded character set (UCS)
ISO/IEC 23092-2, Information technology — Genomic information representation — Part 2: Coding of genomic
information
ISO/IEC 23092-3, Information technology — Genomic information representation — Part 3: Metadata and
application programming interfaces (APIs)
ISO/IEC 23092-6, Information technology — Genomic information representation — Part 6: Coding of genomic
annotations
IETF RFC 3986, Uniform Resource Identifier (URI): Generic Syntax
IETF RFC 7320, URI Design and Ownership
3 Terms and definitions
For the purposes of this document, the following terms and definitions apply.
ISO and IEC maintain terminology databases for use in standardization at the following addresses:
— ISO Online browsing platform: available at https:// www .iso .org/ obp
— IEC Electropedia: available at https:// www .electropedia .org/
3.1
access unit
logical data structure containing a coded representation of genomic information to facilitate bit stream
access and manipulation
3.2
access unit covered region
genomic range comprised between the access unit start position and the access unit end position, inclusive

© ISO/IEC 2025 – All rights reserved
3.3
access unit start position
position of the left-most mapped base among the first alignments of all genomic records contained in the
access unit, irrespective of the strand
3.4
access unit end position
position of the right-most mapped base among the first alignments of all genomic records contained in the
access unit, irrespective of the strand
3.5
access unit range
genomic range comprised between the access unit start position and the right-most genomic record position
among all genomic records contained in the access unit
3.6
alignment
information describing the similarity between a sequence (typically a sequencing read) and a reference
sequence (for instance, a reference genome)
3.7
box
object-oriented building unit defined by a unique type identifier and length
3.8
cluster
aggregation of genomic records
3.9
cluster signature
signature
sequence of nucleotides that is common to most or all genomic records belonging to a cluster
3.10
container box
box (3.8) whose sole purpose is to contain and group a set of related boxes
3.11
data stream
set of packets (3.20) transporting the same data type
3.12
extended access unit start position
position of the left-most mapped base among all alignments of all genomic records contained in the access
unit, irrespective of the strand
3.13
extended access unit end position
position of the right-most mapped base among all alignments of all genomic records contained in the access
unit, irrespective of the strand
3.14
file format
set of data structures for the storage of coded information
3.15
genomic position
position
integer number representing the zero-based position of a nucleotide within a reference sequence

© ISO/IEC 2025 – All rights reserved
3.16
genomic region
region
genomic interval between a start nucleotide position and an end nucleotide position, inclusive
3.17
genomic range
range
interval of positions on a reference sequence defined by a start position s and an end position e such that
s ≤ e; the start and the end positions of a genomic range are always included in the range
3.18
mapped base
base of the aligned read that either matches the corresponding base on the reference sequence or can be
turned into the corresponding base on the reference sequence via a substitution
3.19
packet
transmission unit transporting segments of any of the data structures defined in this document
3.20
reference genome
representative example of the sequences for a species’ genetic material
Note 1 to entry: Genetic material meaning the sequences of the DNA molecules present in a typical cell of that species.
3.21
reference sequence
nucleic acid sequence with biological relevance
Note 1 to entry: Each reference sequence is indexed by a one-dimensional integer coordinate system whereby each
integer within range identifies a single nucleotide. Coordinate values can only be equal to or larger than zero. The
coordinate system in the context of this standard is zero-based (i.e. the first nucleotide has coordinate 0 and it is said
to be at position 0) and linearly increasing within the string from left to right.
3.22
genomic segment
segment
contiguous sequence of nucleotides, typically output of the sequencing process and sequenced from one
strand of a template
3.23
sequence read
read
readout, by a specific technology more or less prone to errors, of a continuous part of a nucleic acid molecule
extracted from an organic sample
3.24
syntax field
element of data represented in the data format
3.25
template
genomic sequence that is produced by a sequencing machine as a single unit
Note 1 to entry: A template can be made of one or more segments, being called single-end sequencing read when it
only has one segment and paired-end sequencing read when it has two segments.
3.26
transport format
set of data structures for the transport of coded information

© ISO/IEC 2025 – All rights reserved
3.27
variable
parameter either inferred from syntax fields or locally defined in a process description
4 Conventions
4.1 Operators and functions
NOTE The operators used in this document are similar to those used in the C programming language. However,
integer division with truncation and rounding are specifically defined. The bitwise operators are defined assuming
two's-complement representation of integers. Numbering and counting loops generally begin from 0.
4.1.1 Arithmetic operators
+ addition
− subtraction (as a binary operator) or negation (as a unary operator)
* multiplication
/ integer division with truncation of the result toward 0 (for example, 7/4 and −7/−4 are truncated
to 1 and −7/4 and 7/−4 are truncated to −1)
4.1.2 Logical operators
|| logical OR
&& logical AND
! logical NOT
x ? y : z If x is TRUE or not equal to 0, evaluates to the value of y; otherwise, evaluates to the value of z.
4.1.3 Relational operators
> greater than
≥ greater than or equal to
< less than
≤ less than or equal to
== equal to
!= not equal to
4.1.4 Bitwise operators
& AND
| OR
>> shift right with sign extension
<< shift left with 0 fill
© ISO/IEC 2025 – All rights reserved
4.1.5 Assignment operators
The following arithmetic operators are defined as follows:
= assignment operator
++ increment, i.e., x++ is equivalent to x = x + 1; when used in an array index, evaluates to the value of
the variable prior to the increment operation.
-- decrement, i.e., x− − is equivalent to x = x − 1; when used in an array index, evaluates to the value
of the variable prior to the decrement operation.
+= increment by amount specified, i.e., x += 3 is equivalent to x = x + 3, and x += (−3) is equivalent
to x = x + (−3).
-= decrement by amount specified, i.e., x −= 3 is equivalent to x = x − 3, and x −= (−3) is equivalent
to x = x − (−3).
4.1.6 String/Character functions and operator
+ string concatenation, when applied on variables of string or character types
4.1.7 Data structure function and operator
sizeof(N) size in bytes of N, where N is either a data structure or a data type
N->m returns the data field m defined within the data structure N
4.1.8 Mathematical functions
The following mathematical functions are defined:
Ceil( x ) the smallest integer greater than or equal to x
Floor( x ) the largest integer less than or equal to x
Log( x ) the base-e logarithm of x
Log2( x ) the base-2 logarithm of x
xx; <= y

Min( x, y )

yx; > y

xx; >= y

Max( x, y )

yx; < y

4.1.9 Array operation functions
array_dims[] = Size(ndimensional_array[]…[], dim) returns the dimensional size(s) of variable ndimensional_
th th
array. If dim is not specified, it returns a vector with the i element corresponding to the size of the i
dimension. If dim is specified, it returns only the size of the dimension corresponding to dim, with 1 being
the first dimension.
Max(x[]) returns the maximum value in a numeric array x[].
Find(x[], v) returns the index of the first element in array x[] that is equal to the value v. It returns -1 if v is
not found.
© ISO/IEC 2025 – All rights reserved
4.2 Syntax and semantics
4.2.1 Method of specifying syntax in tabular form
Table 1 lists the constructs that are used to express the conditions when data elements are present.
NOTE This syntax uses the convention that a variable or expression evaluating to a non-zero value is equivalent
to a condition that is true.
Table 1 — Constructs used to express the conditions when data elements are present
Construct Description
if (condition) {
data_element If the condition is true, then the first group of data
elements occurs next in the bitstream.
. . .
}
else {
data_element If the condition is not true, then the second group of data
elements occurs next in the bitstream.
. . .
}
The group of data elements occurs n times. Conditional
for (i=0; i constructs within the group of data elements may depend on
data_element
the value of the loop control variable i, which is equal
. . .
to zero for the first occurrence, incremented to 1 for the
} second occurrence, and so forth.
As noted, the group of data elements may contain nested conditional constructs. For compactness, the {}
are omitted when only one data element follows. Collections of data elements are represented as listed in
Table 2.
Table 2 — Syntax used to represent collections of data elements
Syntax Description
data_element[] is an array of data. The number of data
data_element[]
elements is indicated by the semantics.
th
data_element[n] data_element[n] is the n element of an array of data.
th th
data_element[m][n] is the m , n element of a two-
data_element[m][n]
dimensional array of data.
th th th
data_element[l][m][n] is the l , m , n element of a
data_element[l][m][n]
three-dimensional array of data.
4.2.2 Bit ordering
The bit order of syntax fields in the syntax tables is specified to start with the most significant bit (MSB) and
proceed to the least significant bit (LSB).
4.2.3 Specification of syntax functions
byte_aligned() is specified as follows:
— If the current position in the bitstream is on a byte boundary, i.e., the next bit in the bitstream is the first
bit in a byte, the return value of byte_aligned() is equal to TRUE.
— Otherwise, the return value of byte_aligned() is equal to FALSE.
read_bits(n) reads the next n bits from the bitstream and advances the bitstream pointer by n bit positions.
When n is equal to 0, read_bits( n ) is specified to return a value equal to 0 and to not advance the bitstream
pointer.
© ISO/IEC 2025 – All rights reserved
The following data types specify the parsing process of each syntax element:
— f(n): fixed-pattern bit string using n bits written (from left to right) with the left bit first. The parsing
process for this data type is specified by the return value of the function read_bits(n).
— u(n): unsigned integer using n bits. When n is "v" in the syntax table, the number of bits varies in a manner
dependent on the value of other syntax elements. The parsing process for this data type
...