ISO/IEC 23092-6:2023 情報技術 | ページ 6

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 start position

position of the leftmost mapped base among the first alignments of all genomic records contained in the access unit, irrespective of the strand

3.3

access unit end position

position of the rightmost mapped base among the first alignments of all genomic records contained in the access unit, irrespective of the strand

3.4

access unit range

genomic range comprised between the access unit start position and the rightmost genomic record position among all genomic records contained in the access unit

3.5

access unit covered region

genomic range comprised between the access unit start position and the access unit end position inclusive

3.6

alignment

information describing the similarity between a sequence (typically a sequencing read) and a reference sequence (for instance, a reference genome)

Note 1 to entry: An alignment is described in terms of a position within the reference, the strand of the reference, and a set of edit operations (matches, mismatches, insertions and deletions, clipping of the sequence ends and splicing information) needed to turn the first sequence into the second.

3.7

allele

each of one or more alternative sequences for a genomic segment

Note 1 to entry: There can be more than one either because the genome contains more than one, almost identical, copies of the same genomic material (2 in the case of humans for all chromosomes from 1 to 22), and/or because one is considering more than one individual in the population.

3.8

annotation record

record

data structure representing a tuple of annotation information (e.g. the properties associated to a variant, a genomic feature or a generic range; it is used also to identify a ”row” when data have matrix format)

3.9

base

base pair

synonymous of nucleotide

3.10

base position

number of bases between a base and the leftmost mapped base belonging to the same genomic segment.

3.11

CIGAR string

CIGAR

textual way of representing an alignment

Note 1 to entry: Several definitions have been used by different programs, the ones referred to here is the one used in the SAM format. It encodes a set of edit operations (matches, mismatches, insertions and deletions, clipping of the sequence ends and splicing information) needed to turn the sequencing read into the reference.

3.12

cluster

aggregation of genomic records

3.13

cluster signature

signature

sequence of nucleotides that is common to most or all genomic records belonging to a cluster

3.14

contig

set of overlapping DNA segments, sequenced and assembled, that together represent a consensus region of DNA

Note 1 to entry: the term “contig” derives from “contiguous”.

3.15

dataset

compression unit containing one or more of: reference sequences; sequencing reads; and alignment information

Note 1 to entry: Datasets are specified in ISO/IEC 23092-1.

3.16

deletion

contiguous removal of one or more bases from a genomic sequence

3.17

E-CIGAR

extended CIGAR syntax specified as a superset of the CIGAR syntax

Note 1 to entry: Among other things, E-CIGAR enables the unambiguous representation of substitutions, spliced reads and splice strandedness.

3.18

edit operation

modification of a sequence of nucleotides by means of a substitution, deletion, insertion or clip

3.19

FASTA

GIR that includes a name and a nucleotide sequence for each sequencing read

Note 1 to entry: Additional information is usually encoded in the read identifier by bioinformatics tools (such as database information, and base calling information).

3.20

FASTQ

GIR that includes FASTA and quality values

3.21

first end

end 1

read 1

first segment of a paired-end template

Note 1 to entry: Illumina platforms usually store first and second ends in two separate files and in the same order – i.e. the n-th read of the first FASTQ file and the n-th read of the second FASTQ file belong to the same template.

3.22

genomic descriptor

descriptor

element of the syntax used to represent a feature of a genomic sequencing read or associated information such as alignment information or quality values

3.23

genomic information representation

way to describe a sequence and some information associated with it

Note 1 to entry: Which information is represented varies depending on the GIR.

3.24

genomic position

position

integer number representing the zero-based position of a nucleotide within a reference sequence

3.25

genomic range

range

interval of positions on a reference sequence specified by a start position s and an end position e such that s ≤ e

Note 1 to entry: The start and the end positions of a genomic range are always included in the range.

3.26

genomic record

record

data structure representing a tuple optionally associated with alignment information, read identifier and quality values

3.27

genomic record index

position of a genomic record in the sequence of genomic records encoded in an access unit

3.28

genomic record position

0-based position of the leftmost mapped base on the reference genome of the first alignment contained in a genomic record

Note 1 to entry: A base present in the aligned read and not present in the reference sequence (insertion) and bases preserved by the alignment process but not mapped on the reference sequence (soft clips) do not have mapping positions.

3.29

genomic reference

reference

collection of reference sequences

Note 1 to entry: Typical examples are a reference genome or a reference transcriptome.

3.30

genomic segment

segment

contiguous sequence of nucleotides

Note 1 to entry: Typically output of the sequencing process, and sequenced from one strand of a template.

3.31

genomic variant

variant

one of the possible sequences for a genomic segment whenever more than one allele for that segment is present

Note 1 to entry: The variant can span one nucleotide (and is then usally called single nucleotide polymorphism) or more (structural variants can involve changes in thousands of contiguous bases or more). A variant can consist of an indel.

3.32

genotype

sequence of a genomic segment for a specified copy of the genome or individual whenever more than one allele for that segment is present

3.33

genotype matrix

metrix specifying which genotype is present in each copy of the genome or individual

3.34

hard clip

one or more bases originally present at either side of a read, and removed from it following alignment

Note 1 to entry: The bases are no longer present in the sequence of the read.

3.35

indel

contiguous stretch of nucleotides that, when aligning two sequences, are inserted into one sequence, or alternatively deleted from the other, in order to make the two sequences the same

Note 1 to entry: From “insertion or deletion”.

3.36

insertion

contiguous addition of one or more bases into a genomic sequence

3.37

leftmost read end

leftmost read

sequencing read generated by a paired-end sequencing run and mapped at a position on the reference sequence which is smaller than the mapping position of the other read in the pair

3.38

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

3.39

nucleotide

monomer of a nucleic acid polymer such as DNA or RNA

Note 1 to entry: Nucleotides are denoted as letters (‘A’ for adenine; ‘C’ for cytosine; ‘G’ for guanine; ‘T’ for thymine which only occurs in DNA; and ‘U’ for uracil which only occurs in RNA). The chemical formula for a specific DNA or RNA molecule is given by the sequence of its nucleotides, which can be represented as a string over the alphabet (‘A’, ’C’, ’G’, ‘T’) in the case of DNA, and a string over the alphabet (‘A’, ‘C’, ‘G’, ‘U’) in the case of RNA. Bases with unknown molecular composition are denoted with ‘N’.

3.40

output annotation record

annotation record produced as output of the decoding process of an annotation table or a portion of it

3.41

paired-end reads

paired-end template

tuple made of two segments

Note 1 to entry: Typically, the segments correspond to the beginning and the end of the same nucleic acid molecule.

3.42

pileup

textual representation of sequencing reads aligned to a reference sequence

3.43

ploidy

number of equivalent alleles present at each position of the genome

3.44

phased genotyping

information about consecutive genotypes along the genome which keeps information about the different copies of the genome (or different individuals) separate, whenever multiple alleles are present

3.45

quality value

quality score

number assigned to each nucleotide base call in automated sequencing processes

Note 1 to entry: Quality values express the base-call accuracy, i.e. the probability (or a related measure) for a nucleotide in the sequence to have been incorrectly determined.

3.46

read group

set of reads having some property in common

3.47

read identifier

read header

read name

text string associated with each sequencing read stored in GIRs such as FASTA, FASTQ and SAM

Note 1 to entry: The read identifier is usually unique within its dataset, and may contain additional information as encoded by bioinformatics tools (such as database information, and base calling information).

3.48

reference genome

representative example of the sequences for a species’ genetic material

Note 1 to entry: Representative of the sequences of the DNA molecules present in a typical cell of that species.

3.49

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.

3.50

rightmost read end

rightmost read

sequencing read generated by a paired-end sequencing run and mapped at a position on the reference sequence which is greater than the mapping position of the other read in the pair

3.51

SAM

GIR that is human readable and includes FASTQ plus alignment and analysis information

Note 1 to entry: From “Sequence Alignment/Map format”. SAM originates from the 1000 Genome Sequencing Project. It is represented in plain ASCII, extensible by users and includes sequence, quality, alignment and analysis information.

3.52

second end

read 2

second segment of a paired-end template

Note 1 to entry: Sequencing platforms usually store first and second ends in two separate files and in the same order – i.e. the n-th read of the first FASTQ file and the n-th read of the second FASTQ file belong to the same template.

3.53

sequencing read

read

readout, by a specific technology more or less prone to errors, of a continuous part of a segment of nucleotides extracted from an organic sample

3.54

single-end read

tuple made of one segment

3.55

SNP

single-nucleotide polymorphism

genomic variant defined as one changed base at a specific position in the genome

3.56

soft clip

soft clipped bases

readone or more bases at either side of the read that have been ignored during the alignment process

Note 1 to entry: The bases are still present in the sequence of the read.

3.57

spliced read

aligned read which, as a consequence of biological splicing, covers non-continuous portions of the reference genome being the result of biological splicing

Note 1 to entry: The read comes from RNA-sequencing and contains at least one junction between two consecutive exons.

3.58

split alignment

aligned paired-end read whose ends are encoded in two different genomic records

3.59

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 – typically they capture both the beginning and the end of a nucleic acid molecule).

3.60

tile

non-syntactic concept describing the AU layout in terms of the original (x,y) coordinates when an annotation file is seen as a bi-dimensional matrix

3.61

tuple

collection of one or more segments

Note 1 to entry: Each segment can be: unmapped; mapped once; or mapped more than once.

3.62

variable

parameter either inferred from syntax fields or locally defined in a process description

3.63

VCF

GIR that is human readable and stores data such as SNPs, insertions, deletions and structural variants of DNA, including annotations.