ABIF File Format

Applied Biosystems Genetic Analysis
Data File Format
September 2009
SUBJECT:
In this document
ABIF File Format Specification and Sample File Schema

This document includes the following topics:
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
A note about support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Important notes about compatibility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
The ABIF file format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Overview of the ABIF format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Detailed structure of the ABIF file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Header . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Directory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Data types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Notes on using the 'user' data type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Sample file schemas . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
ABI PRISM 3100 and 3100-Avant Genetic Analyzer tags . . . . . . . . . . . . . . . . . . . 21
Applied Biosystems 3130/3130xl Genetic Analyzer tags . . . . . . . . . . . . . . . . . . . . 27
Applied Biosystems 3500/3500xl Genetic Analyzer tags . . . . . . . . . . . . . . . . . . . . 33
Applied Biosystems 3730/3730xl DNA Analyzer tags . . . . . . . . . . . . . . . . . . . . . . 44
Applied Biosystems Genetic Analysis Data File Format
Introduction
This document is intended for programmers or bioinformatics groups who wish to
perform additional analysis or other manipulation of ab1 and/or fsa files. The ab1
file is a file type produced by Data Collection software generating sequencing data,
with the extension ".ab1". The fsa file is a file type produced by Data Collection
software generating fragment analysis data, with the extension ".fsa". Both the ab1
and fsa files use the ABIF file format.
The ABIF file format specifies the general rules on how the file is constructed, and
therefore the rules on how it can be read. Elements of data stored in the file are
associated with tags, which are analogous to the keys in a (key, value) mapping.
The ABIF file format by itself does not specify the schema for the ab1 and fsa files,
i.e. which tags are written and when. These schema are specific to the instrument and
software version which created the file.
This user bulletin describes the ABIF format. Following the ABIF specification are
the schemas for each instrument-software combination, for both the ab1 and fsa files
starting on page 21.
Schemas (tables with the valid tags) for the following instruments are given:
ABI PRISM 3100 and 3100-Avant Genetic Analyzer tags (page 21)
Applied Biosystems 3130/3130xl Genetic Analyzer tags (page 27)
Applied Biosystems 3500/3500xl Genetic Analyzer tags (page 33)
Applied Biosystems 3730/3730xl DNA Analyzer tags (page 44)
A note about support

IMPORTANT! Applied Biosystems does not support users of this specification in any
way. Please do not call technical support for addditonal information pertaining to this
specification.
Important notes about compatibility
Important notes about compatibility

Backward and
cross
compatibility
Some tags exist in the ab1 and fsa files for backward compatibility with earlier
versions of Applied Biosystems software. They are no longer used by current
versions of downstream analysis applications.
The ab1 and fsa schema documentation is provided for a specific instrument model
and software version. There is no guarantee that the tagged data described will be
consistent with files produced by earlier software releases and/or other instrument
models.
Forward
compatibility
The critical data in the ab1 and fsa files is stable, and in general new data will extend
the existing schema. However, Applied Biosystems provides no guarantee that all
tagged data elements will be present, consistent, or supported in future versions of
the software, particularly for data that pertains to the details of instrument control or
software integration.
Compatibility of
edited sample files
There are two ways to modify sample files (ab1 and fsa files), either by adding new
tags or changing existing tags. Sample files with new tags added by a user following
Applied Biosystems' instructions as set forth in "Detailed structure of the ABIF file"
on page 7, should continue to be compatible with Applied Biosystems software. Any
modification to sample files by changing the existing tags may result in the file no
longer being compatible with Applied Biosystems software.
IMPORTANT! Applied Biosystems does not recommend any modification of the
software files. Applied Biosystems does not support the editing of sample files in
any way and makes no guarantees as to the compatibility of such files with Applied
Biosystems software.
The ABIF file format

Introduction
The ABIF file format is a binary file format for storing data. Elements of data stored
in the file are associated with tags, which are analogous to the keys in a (key, value)
mapping.
The ABIF format can accommodate a moderate number (<1000) of heterogeneous
data items. A data item can be a scalar value or an array. The basic data types are 8,
16, and 32 bit integers, 32 bit floating-point values, and ASCII characters. There are
also two compound data types: date and time. The data type of each item is identified
by an element type code.
Each data item is uniquely identified (tagged) within a file by a tag name and a tag
number. The tag name and tag number are stored internally as 32-bit integers; the tag
name is intended to be defined as a string of four 8-bit ASCII characters stored in
big-endian order. For example, the tag named ABCD is represented by the hex value
0x41424344. The ABIF format also includes a directory of all the tagged data
elements that are contained in a particular file.
Compatibility goals
Previous versions of ABIF libraries implicitly defined a complex format with many
features that may have been under utilized.
The goal of this user bulletin is to reduce this complexity by creating a restricted
definition that still meets the following goals:
Provide full read and write support for all data types needed by current (2009)
applications.
Provide full read and write support for the thumbprint and boolean legacy data
types.
Provide read and write support for user types only in the form of raw byte
arrays.
Provide read support only for all other legacy data types, only in the form of raw
byte arrays.
Ensure that any file written according to this specification can be read by the
current (2009) Applied Biosystems software.
Ensure that any ABIF file written by an application released during or after
1998 can be read according to this specification.
Eliminate any ambiguity in implementation requirements.
Historical notes
Applied Biosystems modeled the ABIF format after Tag Image File Format (TIFF), a
format for graphics files, and the Macintosh OS Resource Manager. "ABIF" is an
abbreviation of Applied Biosystems, Inc. Format.
The original ABIF specification was written in an era when a typical computer had 1
MB of RAM and operated at 16 MHz. Therefore, the ABIF libraries were designed
to perform input/output operations in several small pieces to minimize the amount of
data resident in RAM at one time.
Overview of the ABIF format
The early ABIF file was expected to also serve as a simple database or nonresident
data structure, since virtual memory was not a feature of the operating system at that
time. The format was originally implemented on the Classic Mac OS, which used
floating blocks of memory called handles. This is the origin of the datahandle field in
ABIF directory entries. The datahandle field is reserved for internal use by libraries;
it has no meaning in the file itself, but it should not be modified or used for any other
purpose. Part of the header area was reserved for managing range-locking of data
items. This was part of a plan to implement multi-user access controls, which were
never implemented.
To avoid the effort involved in rewriting a file from scratch, the original ABIF
specification allowed for multiple, linked tag directories (as does TIFF) so that data
could easily be appended to an existing file. Also like TIFF, ABIF originally allowed
for little-endian (as well as big-endian) byte ordering, which would be indicated by
the order of the letters (A B I F) in the first four bytes of the file. These features were
probably never used, and they have been eliminated from the current specification.
Overview of the ABIF format

Data types
The ABIF format supports storage of the basic low-level data types common to most
programming languages. These include char (a single byte character), short (a two
byte integer), long (a four byte integer), float (a four byte floating point value) and
double (an eight byte floating point value). Data stored as any of these basic types
can be either scalar values or arrays.
In addition, two types of strings are supported. The cString type is a C-style string
(null terminated). The pString type is a Pascal-style string (the length of the string is
stored in the first byte of data). Values stored as pString are required to be less than
256 characters.
Some additional storage formats have been defined and are described below.
Data tags
Tags are used to index the data contained in the file and can be thought of as (name,
number) pairs. In practice, the names are required to be four characters and thus can
always be converted to four-byte integers.
Unique (name, number) combinations define unique tags. For example, tags with the
same name but different numbers are allowed to be of different types and contain
unrelated information.
Data storage
A designated section of the ABIF file contains a directory. The directory entries
contain the tag (name, number) information, data type, number of elements, etc. For
data values that are four bytes or less, the value is stored in the directory entry.
Otherwise, an offset to the binary data in the file is stored. Details of the directory
and binary storage formats are described below.
Detailed structure of the ABIF file
Detailed structure of the ABIF file

The file consists of three logical parts:
Header - discussed below
Directory - discussed on page 10
Data - discussed on page 13
The header area is located at a fixed position at the beginning of the file. The data
and directory areas have no fixed locations.
Although it may be convenient to do so, there is no requirement that the directory be
located at the end of the file. The directory may be located before, after, or in
between other data items, and there may be unused space between items.
All integers in ABIF data structures are stored in big-endian order (high-order byte
first).
In the following descriptions, SInt16 refers to a signed 16-bit integer, UInt8refers to
an unsigned 8-bit integer, etc.
Header
File signature
The header is a 128-byte area at the beginning of the file.

0
1
A
2
B
3
I
The first four bytes of the file are the ASCII codes for A, B, I, F. You
implementations should check these bytes to verify that a file's format is ABIF.
Version number
4
101
The next two bytes comprise a 16-bit integer corresponding to the version number of
the format.
The version number is listed in earlier libraries as being equal to "version number
field x100", suggesting that the current value of 101 would be interpreted as "version
1.1," i.e., the first minor variation number of the first major version.
A common interpretation of major and minor version numbers is that a major version
change indicates a break in code compatibility, while a minor version change
indicates a change only in interpretation or content. Given that, files conforming to
the specification in this document would have a version number of 102, because the
major compatibility is the same, but some obsolete features have been formally
dropped. This is not the case, however. As long as compatibility with Applied
Biosystems software is required, your implementations must continue to write a
value of 101 here.
Your implementations must read this value to check for compatibility between the
file's format and the current version of the library; perform the check by dividing this
value by 100 to get the major version number, and then comparing that value with the
major version of the library. If the values differ, your implementation must return an
error without attempting to read further. If the major version numbers are the same,
reading may continue and it is up to the client application to handle any difference in
minor version number.
Directory entry
structure
The next 28 bytes comprise a single directory entry structure that points to the
directory. A directory entry is a packed structure (no padding bytes) of the following
form:
struct DirEntry{
SInt32 name;
//tag name
SInt32 number;
//tag number
SInt16 elementtype;
//element type code
SInt16 elementsize;
//size in bytes of one element
SInt32 numelements;
//number of elements in item
SInt32 datasize;
//size in bytes of item
SInt32 dataoffset;
//item's data, or offset in file
SInt32 datahandle;
//reserved
Header
The DirEntry Structure is shown schematically below.

6
tdir
10
1
14
16
1023
28
18
num elements
22
data size
26
data offset
30
0
Your implementations which write ABIF should use the values shown above for tag
number, element type and the other items in the DirEntry struct. The directory size
(datasize) should be exactly the size required for the entries (numelements x
elementsize).
Your implementations that read ABIF must extract the numelements field, a
32-bit integer at byte18, and the dataoffset field, a 32-bit integer at byte 26.
These specify the number of entries in the directory and the location of the directory.
The other fields should be ignored.
Note: Previous libraries may have reserved additional space in the directory, and
therefore datasize may be larger than numelements x elementsize.
Unused space in
the header
The DirEntry is followed by 47 2-byte integers, all to be ignored on the input and set
to zero on output.
35
34
36
37
0
0
...
35
34
36
37
0
The original spec reserved these fields to implement range-locking for a multi-user
access scheme, but that feature was never implemented.
Directory
The directory is located at the offset specified in the header, and consists of an array
of directory entries.
directory offset
directory entry #1
directory offset + 28
directory entry #2
directory offset + 56
directory entry #3
...
directory offset + 28 x (N-1)

directory entry #N
Fields in a directory
entry
Each 28-byte entry consists of the following fields:

Name
SInt32 name; // tag name

The name field is defined as an integer but this field should be treated as an array of
four 8-bit ASCII characters. Use printable ASCII characters in the range 0x21 to
0x7E, and it is appropriate to use an mnemonic abbreviation that is descriptive of the
data item.
10
Directory
Tag number
SInt32 number; // tag number

The number field can be any signed 32-bit integer, but it is customary to use
positive values only, beginning with 1. It is also customary to use values less than
1000.
Element type
SInt16 elementtype; // element type code

The elementtype indicates the type of data contained in the data item. New
applications writing ABIF files should only use codes for current data types. (See
"Current data types" on page 13.)
Your implementations should provide for writing user types, but only in the form of
byte-arrays of raw data. The basic library should not provide interpretation or
translation of unsupported types. (You have the option of defining custom user types
in applications, but Applied Biosystems discourages this practice; see "Notes on
using the 'user' data type" on page 19.)
Your implementations should provide for reading all unsupported legacy element
types (including user types >= 1024), but only in the form of byte-arrays of raw data.
No interpretation or translation of unsupported types should be provided in the basic
library. (These types are listed in ""Supported legacy data types" on page 15.)
Your implementations should also provide for editing or copying an existing file that
contains tags with unsupported element types. Implementations should not provide
for editing or creating new individual tags that use an unsupported element type.
If your implementation encounters an undefined element type (neither current nor
legacy), it should report an error to the caller.
Library implementations should not introduce new data types or resurrect legacy data
types.
Element size
SInt16 elementsize; // size in bytes of one element

For all supported data types, the elementsize field is redundant, since the element
size for each type is uniquely defined by the specification. You may use or ignore
this field on input in your implementations, but you must write the correct value on
output.
For user types and unsupported types, ignore this value on input.
Implementations should neither make this field available to client software nor allow
client software to set this value.
11
Number of elements
SInt32 numelements; // number of elements in item

The numelements field gives the number of elements in the data item. Note that
for the string types, an "element" is an individual character, not the string itself.
For user types and unsupported types, ignore this value on input and copy it to the
file on output without use or interpretation.
Item's size
SInt32 datasize; // size in bytes of item

The datasize field gives the number of bytes in the data item.
Offset to item's location
SInt32 dataoffset; // item's data, or offset infile

For data items of size greater than 4 bytes, the dataoffset field contains the
offset to the data in the file. dataoffset field contains the data item itself. In this case,
the data bytes are stored beginning at the high-order byte of the 32-bit field.
Examples:
Data Item
Dataoffset value
one byte with value
15 0x0F000000
two character pString "AB"
0x02414200
array of two shorts {1, 2}
0x00010002
Data handle
SInt32 datahandle; // reserved

Your implementation should ignore the datahandle field on input and write a
value of zero on output. (This field was used in libraries that implemented a virtual
memory system similar to that of the Classic Mac OS Resource manager; see
"Historical notes" on page 4.)
12
Data types
Data types
This specification describes three data types:
Current types (see below)
Legacy data types which should be supported (see page 15 )
Legacy data types which do not need to be supported (see page 16)
Current data types
Name
byte
Element type
Element size
1 byte
Description
Unsigned 8-bit integer.
Name
char
Element type
Element size
1 byte
Description
8-bit ASCII character or signed 8-bit integer
Name
word
Element type
Element size
2 bytes
Description
Unsigned 16-bit integer.
Name
short
Element type
Element size
2 bytes
Description
Signed 16-bit integer.
Name
long
Element type
Element size
4 bytes
Description
Signed 32-bit integer.
13
Name
float
Element type
Element size
4 bytes
Description
32-bit floating point value.
Name
double
Element type
Element size
8 bytes
Description
64-bit floating point value.
Name
date
Element type
10
Element size
4 bytes
Description
Packed structure to represent calendar date:

{
SInt16 year; // 4-digit year
UInt8 month; // month 1-12
UInt8 day; // day 1-31
}
Name
time
Element type
11
Element size
4 bytes
Description
Packed structure to represent time of day:

{
UInt8
UInt8
UInt8
UInt8
hour; // hour 0-23

minute; // minute 0-59
second; // second 0-59
hsecond; // 0.01 second 0-99
14
Data types
Name
pString
Element type
18
Element size
1 byte
Description
Pascal string, consisting of a character count (from 0 to 255) in the

first byte followed by the 8-bit ASCII characters.
Note: Each byte is considered to be an element of the item. The
number of elements in the item is equal to the number of characters
plus one.
Name
cString
Element type
19
Element size
1 byte
Description
C-style string, consisting of a string of 8-bit ASCII characters

followed by a null (zero) byte.
Note: Each byte is considered to be an element of the item. The
number of elements in the item is equal to the number of characters
plus one.
Supported legacy
data types
Name
thumb
Element type
12
Element size
10 bytes
Description
The "thumbprint" structure was intended to provide a unique file

identifier that could be generated on a local (non-networked)
computer and yet would be highly likely to be different from any other
thumbprint structure generated on any other computer.
It is a packed structure of the following form:
{
SInt32 d;
SInt32 u;
UInt8 c;
UInt8 n;
}
15
Unsupported
legacy data types
Name
bool
Element type
13
Element size
1 byte
Description
One-byte boolean value, with zero meaning false and any other value
meaning true.
Name
user
Element type
1024 or greater
Element size
1 byte
Description
A user-defined data structure. The product of the numelements

and elementsize fields may not be equal to the datasize
field.
Name
rational
Element type
Element size
8 bytes
Description
Packed structure to describe an integer fraction:
{
SInt32 numerator;
SInt32 denominator
}
16
Name
BCD
Element type
Element size
unknown
Description
Binary-coded decimal value of unknown format.
Data types
Name
point
Element type
14
Element size
4 bytes
Description
Packed structure to describe a point, using 16-bit coordinates:
{
SInt16 v;
SInt16 h;
}
Name
rect
Element type
15
Element size
8 bytes
Description
Packed structure to describe a rectangle, using 16-bit coordinates:
{
SInt16
SInt16
SInt16
SInt16
top;
left;
bottom;
right;
Name
vPoint
Element type
16
Element size
8 bytes
Description
Packed structure to describe a point, using 32-bit coordinates:
{
SInt32 v;
SInt32 h;
}
17
Name
vRect
Element type
17
Element size
16 bytes
Description
Packed structure to describe a rectangle, using 32-bit coordinates:
{
SInt32
SInt32
SInt32
SInt32
top;
left;
bottom;
right;
Name
Tag
Element type
20
Element size
8 bytes
Description
Packed structure to describe an ABIF tag:
{
SInt32 name;
SInt32 number;
}
18
Name
deltaComp
Element type
128
Element size
Description
Compressed data.
Name
LZWComp
Element type
256
Element size
Description
Compressed data.
Notes on using the 'user' data type
Name
deltaLZW
Element type
384
Element size
Description
Compressed data.
Notes on using the 'user' data type

Applications have used the user data type (element type >= 1024) to store opaque
OS-specific data structures (such as the Mac OS alias) or compound C or Pascal data
structures. This use of user type has caused some difficulties in the past when
operating systems and/or compilers have changed, due to dependencies on how a
particular language and/or compiler represents that data in memory. Your
implementations should avoid using the user data type in this manner, to eliminate
such problems in the future. When you need to store any user-defined data type, such
as a struct or an array of structs, break it into arrays of individual fields, rather than
using the user data type.
For example, consider the following structure to be stored.
struct FooStruct {
SInt8 alpha;
SInt16 beta;
SInt32 gamma;
} [5]
To store this, DO NOT define a user type and create one data item, as shown below.
Name
FooS
Number
42
Element type
user
Element size
12
Num elements
Instead, use three separate data items, one for each field, as shown below:
Name
Alph
Number
42
Element type
byte
Element size
Num elements
19
Name
Beta
Number
42
Element type
short
Element size
Num elements
Name
Gamm
Number
42
Element type
long
Element size
Num elements
Sample file schemas

This section contains the tags for ab1 and fsa files generated by the various
instrument-software combinations, grouped by instrument and then software version.
Optional tags are shown in italic text.
Additional tags that are added to the ab1 files during analysis by SeqScape and/or
Sequencing Analysis software are also listed, starting on page 56.
Note: ab1 and fsa files generated by future versions of Data Collection software may
contain additional tags or the contents and/or format of the existing tags may be
modified.
20
ABI PRISM 3100 and 3100-Avant Genetic Analyzer tags

Tags in this section
Table 1: ab1 File Tags from ABI PRISM 3100/3100-Avant Analyzer Data Collection
Software v2.0 on the ABI PRISM 3100/3100-Avant Genetic Analyzer (below)
Table2: fsa File Tags from ABI PRISM 3100/3100-Avant Analyzer Data Collection
Software v2.0 on the ABI PRISM 3100/3100-Avant Genetic Analyzer (page 24)
Table 1 ab1 File Tags from ABI PRISM 3100/3100-Avant Analyzer Data
Collection Software v2.0 on the ABI PRISM 3100/3100-Avant Genetic Analyzer
Name
Number
ABIF Type
Description
APFN
pString
Sequencing Analysis parameters file name
APXV
cString
Analysis Protocol XML schema version
APrN
cString
Analysis Protocol settings name
APrV
cString
Analysis Protocol settings version
APrX
char
CMNT
pString
Comment about sample (optional)
CTID
cString
Container identifier, aka. plate barcode
CTNM
cString
Container name (usually identical to CTID)
CTTL
pString
Comment title
CpEP
char
Is Capillary Machine?
DATA
short
Channel 1 raw data
DATA
short
Channel 2 raw data
DATA
short
Channel 3 raw data
DATA
short
Channel 4 raw data
DATA
short
Voltage, measured (decavolts)
DATA
short
Current, measured (milliAmps)
DATA
short
Power, measured (milliWatts)
DATA
short
Temperature, measured (degrees C)
DATA
105
short
Raw data for dye 5 (optional)
DSam
short
Downsampling factor
DySN
pString
Dye#
short
DyeN
pString
Dye 1 name
DyeN
pString
Dye 2 name
DyeN
pString
Dye 3 name
DyeN
pString
Dye 4 name
Analysis Protocol XML string
Dye set name

Number of dyes
21
Name
Number
ABIF Type
DyeW
short
Dye 1 wavelength
DyeW
short
Dye 2 wavelength
DyeW
short
Dye 3 wavelength
DyeW
short
Dye 4 wavelength
EPVt
long
Electrophoresis voltage setting (volts)
EVNT
pString
Start Run event
EVNT
pString
Stop Run event
EVNT
pString
Start Collection event
EVNT
pString
Stop Collection event
FWO_
char
GTyp
pString
InSc
long
Injection time (seconds)
InVt
long
Injection voltage (volts)
LANE
short
Lane/Capillary
LIMS
pString
Sample tracking ID
LNTD
short
Length to detector
LsrP
long
Laser Power setting (micro Watts)
MCHN
pString
Instrument name and serial number
MODF
pString
Data collection module file
MODL
char
Model number
NAVG
short
Pixels averaged per lane
NLNE
short
Number of capillaries
OfSc
long
List of scans that are marked off scale in Collection. (optional)
OvrI
1-N
long
One value for each dye. List of scan number indices for scans with color
data values >32767. Values cannot be greater than 32000. (optional)
OvrV
1-N
long
One value for each dye. List of color data values for the locations listed in
the OvrI tag. Number of OvrV tags must be equal to the number of OvrI
tags. (optional)
PDMF
pString
PXLB
long
RGCm
cString
Results group comment (optional)
RGNm
cString
Results group name
RMXV
cString
Run Module XML schema version
RMdN
cString
Run Module name (same as MODF)
RMdV
cString
Run Module version
RMdX
char
22
Description
Base order
Gel type description
Mobility file (orig)

Pixel bin size
Run Module XML string

Name
Number
ABIF Type
Description
RPrN
cString
Run Protocol name
RPrV
cString
Run Protocol version
RUND
date
Run start date
RUND
date
Run stop date
RUND
date
Data Collection start date
RUND
date
Data Collection stop date
RUNT
time
Run start time
RUNT
time
Run stop time
RUNT
time
Data Collection start time
RUNT
time
Data Collection stop time
Rate
user
Scanning rate
RunN
cString
SCAN
long
SMED
pString
Polymer lot expiration date
SMLt
pString
Polymer lot number
SMPL
pString
Sample name
SVER
pString
Data collection software version
SVER
pString
Data collection firmware version
Satd
long
Array of longs representing the scan numbers of data points, which are
flagged as saturated by data collection (optional)
Scal
float
Rescaling divisor for color data
Scan
short
Number of scans (legacy - use SCAN)
TUBE
pString
Tmpr
long
User
pString
Run Name
Number of scans
Well ID
Run temperature setting
Name of user who created the plate (optional)
23
Table 2 fsa File Tags from ABI PRISM 3100/3100-Avant Analyzer Data Collection
Software v2.0 on the ABI PRISM 3100/3100-Avant Genetic Analyzer
Name
Number
ABIF Type
ANME
cString
GeneMapper software analysis method name
CMNT
1-N
pString
Comment(s) about sample (optional)
CTID
cString
Container identifier (plate barcode, for example)
CTNM
cString
CTTL
pString
Comment title
CpEP
char
DATA
short
Channel 1 raw data
DATA
short
Channel 2 raw data
DATA
short
Channel 3 raw data
DATA
short
Channel 4 raw data
DATA
short
DATA
short
DATA
short
DATA
short
DATA
105
short
DSam
short
Downsampling factor
DySN
pString
Dye#
short
Number of dyes
DyeB
char
Dye 1 significance S for standard, space for sample
DyeB
char
DyeB
char
DyeB
char
DyeB
char
Dye 5 significance S for standard, space for sample (optional)
DyeN
pString
Dye 1 name
DyeN
pString
Dye 2 name
DyeN
pString
Dye 3 name
DyeN
pString
Dye 4 name
DyeN
pString
Dye 5 name (optional)
DyeW
short
Dye 1 wavelength
DyeW
short
Dye 2 wavelength
DyeW
short
Dye 3 wavelength
DyeW
short
Dye 4 wavelength
DyeW
short
Dye 5 wavelength (optional)
24
Description
Dye set name
Name
Number
ABIF Type
Description
EPVt
long
EVNT
pString
Start Run event
EVNT
pString
Stop Run event
EVNT
pString
EVNT
pString
GTyp
pString
InSc
long
InVt
long
LANE
short
Lane/Capillary
LIMS
pString
Sample tracking ID
LNTD
short
Length to detector
LsrP
long
MCHN
pString
MODF
pString
MODL
char
Model number
NAVG
short
NLNE
short
OfSc
long
OvrI
1-N
long
OvrV
1-N
long
tags. (optional)
PANL
cString
PXLB
long
RGCm
cString
RGNm
cString
Results group name
RMXV
cString
RMdN
cString
RMdV
cString
Run Module version
RMdX
char
RPrN
cString
Run Protocol name
RPrV
cString
RUND
date
Run start date
RUND
date
Run stop date
RUND
date
GeneMapper software panel name

Pixel bin size
25
Name
Number
ABIF Type
RUND
date
RUNT
time
Run start time
RUNT
time
Run stop time
RUNT
time
RUNT
time
Rate
user
Scan rate
RunN
cString
Run Name
SCAN
long
SMED
pString
SMLt
pString
Polymer lot number
STYP
cString
GeneMapper software Sample Type
SVER
pString
SVER
pString
SVER
pString
Sample File Format Version, containing the version of the sample file
format used to write the file
Satd
long
Scal
float
Scan
short
SpNm
pString
Sample name for Genescan software sample files
StdF
pString
Size Standard file name
TUBE
pString
Well ID
Tmpr
long
User
pString
26
Description
Number of scans

Applied Biosystems 3130/3130xl Genetic Analyzer tags

Tags in This
Table 3: ab1 File Tags from Applied Biosystems 3130/3130xl Data Collection
Software v3.0 on the Applied Biosystems 3130/3130xl Genetic Analyzer (below)
Table 4: fsa File Tags from Applied Biosystems 3130/3130xl Data Collection
Software v3.0 on the Applied Biosystems 3130/3130xl Genetic Analyzer (page 30)
Table 3 ab1 File Tags from Applied Biosystems 3130/3130xl Data Collection
Software v3.0 on the Applied Biosystems 3130/3130xl Genetic Analyzer
Name
Number
ABIF Type
Description
APFN
pString
APXV
cString
APrN
cString
APrV
cString
APrX
char
CMNT
pString
CTID
cString
CTNM
cString
CTOw
cString
Container owner
CTTL
pString
Comment title
CpEP
char
DATA
short
Channel 1 raw data
DATA
short
Channel 2 raw data
DATA
short
Channel 3 raw data
DATA
short
Channel 4 raw data
DATA
short
DATA
short
DATA
short
DATA
short
DATA
105
short
DSam
short
Downsampling factor
DySN
pString
Dye#
short
DyeN
pString
Dye 1 name
DyeN
pString
Dye 2 name
DyeN
pString
Dye 3 name
Dye set name

Number of dyes
27
Name
Number
ABIF Type
DyeN
pString
DyeW
short
Dye 1 wavelength
DyeW
short
Dye 2 wavelength
DyeW
short
Dye 3 wavelength
DyeW
short
Dye 4 wavelength
EPVt
long
EVNT
pString
Start Run event
EVNT
pString
Stop Run event
EVNT
pString
EVNT
pString
FWO_
char
GTyp
pString
HCFG
cString
Instrument Class
HCFG
cString
Instrument Family
HCFG
cString
Official Instrument Name
HCFG
cString
Instrument Parameters
InSc
long
InVt
long
LANE
short
Lane/Capillary
LIMS
pString
Sample tracking ID
LNTD
short
Length to detector
LsrP
long
MCHN
pString
MODF
pString
MODL
char
Model number
NAVG
short
NLNE
short
OfSc
long
OvrI
1-N
long
OvrV
1-N
long
tags. (optional)
PDMF
pString
PXLB
long
RGCm
cString
28
Description
Dye 4 name
Base order

Pixel bin size
Name
Number
ABIF Type
Description
RGNm
cString
Results group name
RMXV
cString
RMdN
cString
RMdV
a1
cString
Run Module version
RMdX
char
RPrN
cString
Run Protocol name
RPrV
cString
RUND
date
Run start date
RUND
date
Run stop date
RUND
date
RUND
date
RUNT
time
Run start time
RUNT
time
Run stop time
RUNT
time
RUNT
time
Rate
user
Scanning rate
RunN
cString
SCAN
long
SMED
pString
SMLt
pString
Polymer lot number
SMPL
pString
Sample name
SVER
pString
SVER
pString
Satd
long
Scal
float
Scan
short
TUBE
pString
Tmpr
long
User
pString
Run Name
Number of scans
Well ID
29
Table 4 fsa File Tags from Applied Biosystems 3130/3130xl Data Collection
Name
Number
ABIF Type
1-N
pString
CTID
cString
CTNM
cString
CTOw
cString
Container owner
CTTL
pString
Comment title
CpEP
char
DATA
short
Channel 1 raw data
DATA
short
Channel 2 raw data
DATA
short
Channel 3 raw data
DATA
short
Channel 4 raw data
DATA
short
DATA
short
DATA
short
DATA
short
DATA
105
short
DCHT
short
Detector Cell Heater Temperature
DSam
short
Downsampling factor
DySN
pString
Dye#
short
Number of dyes
DyeB
char
DyeB
char
DyeB
char
DyeB
char
DyeB
char
DyeN
pString
Dye 1 name
DyeN
pString
Dye 2 name
DyeN
pString
Dye 3 name
DyeN
pString
Dye 4 name
DyeN
pString
DyeW
short
Dye 1 wavelength
DyeW
short
Dye 2 wavelength
DyeW
short
Dye 3 wavelength
DyeW
short
Dye 4 wavelength
CMNT
30
Description
Dye set name
Name
Number
ABIF Type
Description
DyeW
short
EPVt
long
EVNT
pString
Start Run event
EVNT
pString
Stop Run event
EVNT
pString
EVNT
pString
GTyp
pString
HCFG
cString
Instrument Class
HCFG
cString
Instrument Family
HCFG
cString
HCFG
cString
InSc
long
InVt
long
LANE
short
Lane/Capillary
LIMS
pString
Sample tracking ID
LNTD
short
Length to detector
LsrP
long
MCHN
pString
MODF
pString
MODL
char
Model number
NAVG
short
NLNE
short
OfSc
long
OvrI
1-N
long
OvrV
1-N
long
tags. (optional)
PANL
cString
PSZE
long
PTYP
cString
PXLB
long
RGCm
cString
RGNm
cString
Results group name
RMXV
cString

Plate size. The number of sample positions in the container; allowed
values 96 and 384
Plate type. Allowed values are 96-Well, 384-Well.
Pixel bin size
31
Name
Number
ABIF Type
RMdN
cString
RMdV
cString
Run Module version
RMdX
char
RPrN
cString
Run Protocol name
RPrV
cString
RUND
date
Run start date
RUND
date
Run stop date
RUND
date
RUND
date
RUNT
time
Run start time
RUNT
time
Run stop time
RUNT
time
RUNT
time
Rate
user
Scan rate
RunN
cString
Run Name
SCAN
long
SMED
pString
SMLt
pString
Polymer lot number
SVER
pString
SVER
pString
SVER
pString
Satd
long
Scal
float
Scan
short
SpNm
pString
TUBE
pString
Well ID
Tmpr
long
User
pString
32
Description
Number of scans


Software v3.0 on the Applied Biosystems 3500/3500xl Genetic Analyzer (page 39)
Table 5 abi File Tags from Applied Biosystems 3500/3500xl Genetic Analyzer
Data Collection Software v1.0 on the Applied Biosystems 3500/3500xl Genetic
Analyzer
Name
Number
ABIF Type
Description
AAct
boolean
Primary Analysis Audit Active indication. True if system auditing was

enabled during the last write of this file, false if system auditing was
disabled.
ABED
cString
Anode buffer expiration date using ISO 8601 format using the patterns
YYYY-MM-DDTHH:MM:SS.ss+/-HH:MM. Hundredths of a second are
optional.
ABID
cString
Anode buffer tray first installed date
ABLt
cString
Anode buffer lot number
ABRn
long
Number of runs (injections) processed with the current Anode Buffer

(runs allowed - runs remaining)
ABTp
cString
AEPt
short
Analysis Ending scan number for basecalling on initial analysis
Anode buffer type
AEPt
short
Analysis Ending scan number for basecalling on last analysis
AmbT
short[]
Record of ambient temperature readings
APCN
cString
Amplicon name
APFN
pString
Sequencing Analysis parameters file name (same as APrN) (optional)
APrN
cString
Analysis Protocol Settings Name
APrV
cString
Analysis Protocol Settings Version
APrX
char[]
APXV
cString
ARTN
long
Analysis Return code. Produced only by 5 Prime basecaller 1.0b3
ASPF
short
Flag to indicate whether adaptive processing worked or not
Analysis Protocol XML String

Analysis Protocol XML Schema Version
ASPt
short
Analysis Starting scan number for first analysis
ASPt
short
Analysis Starting scan number for last analysis
AsyN
cString
AsyC
char[]
AsyV
cString
AUDT
char[]
AVld
cString
B1Pt
short
The assay name

The assay contents (xml format)
The assay version
Audit log used across 3500 software (optional)
Assay validation flag (true or false)
Reference scan number for mobility and spacing curves for first analysis
33
Name
Number
ABIF Type
Description
B1Pt
short
Reference scan number for mobility and spacing curves for last analysis
BcRn
long
Basecalling qc code
BcRs
cString
Basecalling warnings, a concatenated comma separated string
BcRs
cString
Basecalling errors, a concatenated comma separated string
BCTS
pString
Basecaller timestamp. Time of completion of most recent analysis
CAED
cString
Capillary array expiration
CALt
cString
Capillary array lot number
CARn
long
CASN
cString
Capillary array serial number
CBED
cString
Cathode buffer expiration date
CBID
cString
Cathode buffer tray first installed date
CBLt
cString
Cathode buffer lot number
CBRn
long
CBTp
cString
Cathode buffer type
CkSm
cString
File checksum
CLRG
long
Start of the clear range (inclusive).
CLRG
long
Clear range length
CMNT
pString
Sample Comment
CpEP
byte
Capillary type electrophoresis. 1 for a capillary based machine. 0 for a

slab gel based machine.
CRLn
long
Contiguous read length
CRLn
cString
One of "Pass", "Fail", or "Check"
CTID
cString
Container Identifier, a.k.a. plate barcode
Number of injections processed (including the one of which this sample

was a part) through the capillary array
Number of runs (injections) processed with the current Cathode Buffer

CTNM
cString
Container name, usually identical to CTID, but not necessarily so
CTOw
cString
The name entered as the Owner of a plate, in the plate editor
CTTL
pString
Comment Title
DATA
1-4, 105199
short[]
Short Array holding raw color data
DATA
short[]
Short Array holding measured volts/10 (EP voltage) during run
DATA
short[]
Short Array holding measured milliAmps trace (EP current) during run
DATA
short[]
Short Array holding measured milliWatts trace (Laser EP Power) during

run
DATA
short[]
Short Array holding measured oven Temperature (polymer temperature)

trace during run
DATA
9-12, 205299
short[]
Short Array holding analyzed color data
DCEv
cString
A list of door-close events, separated by semicolon. Door open events

are generally paired with door close events.
DCHT
short
34
Reserved for backward compatibility. The detection cell heater

temperature setting from the Run Module. Not used for 3500.
Name
Number
ABIF Type
Description
DOEv
cString
DSam
short
Downsampling rate
Dye#
short
Number Of Dyes
A list of door-open events, separated by semicolon. Door close events

are generally paired with door open events.
DyeN
1-N
pString
DyeW
1-N
short
DySN
pString
ESig
char[]
EVNT
pString
Start Run Event
EPVt
Dye Name
Dye wavelength
Dye Set Name
long
Electronic signature record used across 3500 software
EVNT
pString
Stop Run Event
EVNT
pString
Start Collection Event
EVNT
pString
Stop Collection Event
Feat
Features. Can be created by Nibbler for Clear Range.
FTab
Feature table. Can be created by Nibbler for Clear Range.
FVoc
Feature table vocabulary. Can be created by Nibbler for Clear Range.
FWO_
char[]
GTyp
pString
Sequencing Analysis Filter wheel order. Fixed for 3500 at "GATC"

Gel or polymer Type
HCFG
cString
The Instrument Class. All upper case, no spaces. Initial valid value: CE
HCFG
cString
The Instrument Family. All upper case, no spaces. Valid values: 31XX or
37XX for UDC, 35XX (for 3500)
HCFG
cString
The official instrument name. Mixed case, minus any special formatting.
Initial valid values: 3130, 3130xl, 3730, 3730xl, 3500, 3500xl.
HCFG
cString
Instrument parameters. Contains key-value pairs of instrument

configuration information, separated by semicolons. Four parameters
are included initially: UnitID=<UNITD number>, CPUBoard=<board
type>, ArraySize=<# of capillaries>, SerialNumber=<Instrument Serial#>.
InjN
cString
Injection name
InSc
long
Injection time setting in Seconds
InVt
long
Injection Voltage setting in Volts
LANE
short
Sample's lane or capillary number
LAST
cString
Parameter settings information
LIMS
pString
Sample Tracking ID
LNTD
short
Length To Detector (capillary length)
LsrP
long
Laser power setting in micro Watts
MCHN
pString
Machine Name. (instrument serial number can be found in HCFG-4)
MODF
pString
Run Module filename. This is redundant with the new tag RMdN
MODL
char[]
Model number. 4 characters
NAVG
short
Number of columns averaged during collection (fixed at 1 for 3500)
NLNE
short
Total number of capillaries
35
Name
Number
ABIF Type
Description
NOIS
float[]
The estimate of rms baseline noise (S/N ratio) for each dye for a
successfully analyzed sample. Corresponds in order to the raw data in
tags DATA 1-4. KB basecaller only.
OfSc
long[]
List of scan numbers that are offscale (optional)
OvrI
1-N
long[]
One for each dye (unanalyzed and/or analyzed data). List of scan
number indexes that have values greater than 32767 but did not saturate
the camera. In Genemapper samples, this can have indexes with values
greater than 32000. In sequencing samples, this cannot have indexes
with values greater than 32000.
OvrV
1-N
long[]
One for each dye (unanalyzed and/or analyzed data). List of color data
values found at the locations listed in the OvrI tag. Optional. There must
be exactly as many numbers in this array as in the OvrI array.
P1RL
short[]
Deviation of primary peak position from (PLoc,2), times 100, rounded to

integer
P1AM
short[]
Amplitude of primary peak, which is not necessarily equal to

corresponding signal strength at that position
P1WD
short[]
Full-width Half-max of primary peak, times 100, rounded to integer.

Corresponding signal intensity is not necessarily equal to one half of
primary peak amplitude
P2BA
char[]
Base of secondary peak
P2RL
short[]
Deviation of secondary peak position from (PLoc,2), times 100, rounded

to integer
P2AM
short[]
Amplitude of secondary peak, which is not necessarily equal to

corresponding signal strength at that position
PBAS
char[]
Array of sequence characters edited by user
PBAS
char[]
Array of sequence characters as called by Basecaller
PCON
char[]
Array of quality Values (0-255) as edited by user
PCON
char[]
Array of quality values (0-255) as called by Basecaller
PDMF
pString
Sequencing Analysis Mobility file name chosen in collection
PDMF
pString
Mobility file name chosen in most recent analysis (identical to PDMF1)
phAR
float
phCH
pString
Chemistry type ("term", "prim", "unknown"), based on DYE_1

information
phDY
pString
Dye ("big", "d-rhod", "unknown"), based on mob file information
Trace peak aria ratio
phQL
short
Maximum Quality Value
phTR
short
Set Trim region
phTR
float
Trim probability
PLOC
short[]
Array of peak locations edited by user
PLOC
short[]
Array of peak locations as called by Basecaller
PROJ
cString
SeqScape 2.0 project name
PRJT
cString
SeqScape 2.0 project template name
PSZE
long
PTYP
cString
PuSc
long
36
Plate size. The number of sample positions in the container. Current

allowed values: 96, 384.
Plate type. Current allowed values: 96-Well, 384-Well.
Median pupscore
Name
Number
ABIF Type
Description
PXLB
long
QcPa
cString
QcRn
long
QcRs
cString
QC warnings, a concatenated comma separated string
QcRs
cString
QC errors, a concatenated comma separated string
QV20
long
QV20
cString
Rate
User type
RevC
RGCm
cString
Results Group comment. Not used for 3500. Reserved to preserve

backward compatibility.
RGNm
cString
Results Group name
RGOw
cString
The name entered as the Owner of a Results Group, in the Results Group
Editor. Implemented as the user name from the results group.
RInj
long
Reinjection number. The reinjection number that this sample belongs to.
Not present if there was no reinjection.
Raman normalization factor
Pixel bin size. Currently limited to values of either 1 or 3.

QC parameters
Trimming and QC code
QV20+ value
Scanning Rate. Milliseconds per frame.
Flag for whether the sequence has been complemented
RNmF
float
RMdN
cString
Module Name. This is redundant with MODF
RMdV
cString
Run Module Version
RMdX
char[]
RMXV
cString
Run Module XML String

Run Module XML Schema Version
RPrN
cString
Run Protocol Name
RPrV
cString
Run Protocol Version
RUND
date
Run Started Date
RUNT
time
Run Started Time
RUND
date
Run Stopped Date
RUNT
time
Run Stopped Time
RUND
date
Data Collection Started Date
RUNT
time
Data Collection Started Time
RUND
date
Data Collection Stopped date
RUNT
time
Data Collection Stopped Time
RunN
cString
Satd
long[]
List of scan indexes which were saturated in the camera.
Run name (which, for 3500, is different from injection name)
Scal
float
Rescaling Divisor for reducing the dynamic range of the color data
SCAN
long
Number of scans. Redundant with Scan, but higher range.
Scan
short
ScPa
cString
ScSt
long
S/N%
short[]
Signal strength for each dye
SMED
pString
Separation Medium Lot Exp Date.
Number of scans. Redundant with SCAN, but lower range. (legacy)

The parameter string of size caller
Raw data start point. Set to 0 for 3500 data collection.
37
Name
Number
ABIF Type
Description
SMID
cString
Polymer first installed date
SMLt
pString
Separation Medium Lot Number (polymer lot number)
SMPL
pString
Sequencing Analysis Sample Name
SMRn
long
Number of runs (injections) processed with the current polymer (runs

allowed - runs remaining)
SPAC
float
Average peak spacing used in last analysis
SPAC
pString
SPAC
float
SPEC
cString
Sequencing Analysis Specimen Name
SpeN
cString
Active spectral calibration name
Basecaller name - corresponds to name of bcp file.

Average peak spacing last calculated by the Basecaller.
SVER
pString
Data Collection version number
SVER
pString
Basecaller version number
SVER
pString
Firmware version number
SVER
pString
Sample File Format Version String
Tmpr
long
TrPa
cString
Oven Temperature setting in degrees C

Timming parameters
TrSc
long
TrSc
cString
TUBE
pString
Autosampler position (A1-H1) (CapEP only)
User
pString
The name of the plate creator
38
Trace score.
Table 6 fsa File Tags from Applied Biosystems 3500/3500xl Genetic Analyzer
Data Collection Software v1.0 on the Applied Biosystems 3500/3500xl Genetic
Analyzer
Name
Number
ABIF Type
Description
AAct
boolean
Primary Analysis Audit Active indication. True if system auditing was

enabled during the last write of this file, false if system auditing was
disabled.
ABED
cString
Anode buffer expiration date using ISO 8601 format using the patterns
YYYY-MM-DDTHH:MM:SS.ss+/-HH:MM. Hundredths of a second are
optional.
ABID
cString
Anode buffer tray first installed date
ABLt
cString
Anode buffer lot number
ABRn
long
Number of runs (injections) processed with the current Anode Buffer

ABTp
cString
Anode buffer type
AmbT
short[]
Record of ambient temperature readings
Anld
boolean
Flag for whether or not a sample has been analyzed
ANME
cString
GeneMapper Analysis method Name. (from secondary analysis protocol,

if defined).
APrN
cString
Analysis Protocol Settings Name
APrV
cString
Analysis Protocol Settings Version
APrX
char[]
Analysis Protocol XML String
APXV
cString
Analysis Protocol XML Schema Version
AsyN
cString
The assay name
AsyC
char[]
The assay contents (xml format)
AsyV
cString
The assay version.
AUDT
char[]
Audit log used across 3500 software
AVld
cString
Assay validation flag (true or false)
CAED
cString
Capillary array expiration
CALt
cString
Capillary array lot number
CARn
long
Number of injections processed (including the one of which this sample

was a part) through the capillary array
CASN
cString
Capillary array serial number
CBED
cString
Cathode buffer expiration date
CBID
cString
Cathode buffer tray first installed date
CBLt
cString
Cathode buffer lot number
CBRn
long
Number of runs (injections) processed with the current Cathode Buffer

CBTp
cString
Cathode buffer type
CkSm
cString
File checksum
CMNT
pString
Sample Comment
CpEP
byte
Capillary type electrophoresis. 1 for a capillary based machine. 0 for a

slab gel based machine.
CTID
cString
Container Identifier, a.k.a. plate barcode
39
Name
Number
ABIF Type
Description
CTNM
cString
Container name, usually identical to CTID, but not necessarily so
CTOw
cString
The name entered as the Owner of a plate, in the plate editor
CTTL
pString
Comment Title
DATA
1-4, 105199
short[]
Short Array holding raw color data
DATA
short[]
Short Array holding measured volts/10 (EP voltage) during run
DATA
short[]
Short Array holding measured milliAmps trace (EP current) during run
DATA
short[]
Short Array holding measured milliWatts trace (Laser EP Power) during

run
DATA
short[]
Short Array holding measured oven Temperature (polymer temperature)

trace during run
DATA
9-12
short[]
Short Array holding analyzed color data
DCEv
cString
A list of door-close events, separated by semicolon. Door open events

are generally paired with door close events.
DCHT
short
Reserved for backward compatibility. The detection cell heater

temperature setting from the Run Module. Not used for 3500.
DOEv
cString
A list of door-open events, separated by semicolon. Door close events

are generally paired with door open events.
DSam
short
Downsampling rate
Dye#
short
Number Of Dyes
DyeN
1-N
pString
Dye Name
DyeW
1-N
short
Dye wavelength
DySN
pString
Dye Set Name
long
EPVt
ESig
char[]
Electronic signature record used across 3500 software (optional)
EVNT
pString
Start Run Event
EVNT
pString
Stop Run Event
EVNT
pString
Start Collection Event
EVNT
pString
Stop Collection Event
FWO_
char[]
Sequencing Analysis Filter wheel order. Fixed for 3500 at "GATC"
GTyp
pString
Gel or polymer Type
HCFG
cString
The Instrument Class. All upper case, no spaces. Initial valid value: CE
HCFG
cString
The Instrument Family. All upper case, no spaces. Valid values: 31XX or
37XX for UDC, 35XX (for 3500)
HCFG
cString
The official instrument name. Mixed case, minus any special formatting.
Initial valid values: 3130, 3130xl, 3730, 3730xl, 3500, 3500xl.
HCFG
cString
Instrument parameters. Contains key-value pairs of instrument

configuration information, separated by semicolons. Four parameters
are included initially: UnitID=<UNITD number>, CPUBoard=<board
type>, ArraySize=<# of capillaries>, SerialNumber=<Instrument Serial#>.
InjN
cString
Injection name.
InSc
long
Injection time setting in Seconds
InVt
long
Injection Voltage setting in Volts
40
Name
Number
ABIF Type
Description
LANE
short
Sample's lane or capillary number
LIMS
pString
Sample Tracking ID
LNTD
short
Length To Detector (capillary length)
LsrP
long
Laser power setting in micro Watts.
MCHN
pString
Machine Name. (instrument serial number can be found in HCFG-4)
MODF
pString
Run Module filename. This is redundant with the new tag RMdN
MODL
char[]
Model number. 4 characters
NAVG
short
Number of columns averaged during collection (fixed at 1 for 3500)
NLNE
short
Total number of capillaries
NrmF
1-N
double
Normalization factor for each dye
NrmS
double
In Lane Size Standard normalization factor
OffS
cString
The off-scale data separated by semi-colon(;). Each data consists of five

numbers separated by comma: start data point, end data point, start
base, end base, and validity
OfSc
long[]
List of scan numbers that are offscale (optional)
OvrI
1-N
long[]
One for each dye (unanalyzed and/or analyzed data). List of scan
number indexes that have values greater than 32767 but did not saturate
the camera. In Genemapper samples, this can have indexes with values
greater than 32000. In sequencing samples, this cannot have indexes
with values greater than 32000.
OvrV
1-N
long[]
One for each dye (unanalyzed and/or analyzed data). List of color data
values found at the locations listed in the OvrI tag. Optional. There must
be exactly as many numbers in this array as in the OvrI array.
PANL
cString
GeneMapper Panel Name. (from secondary analysis protocol, if defined)
PANm
cString
Name of size/base caller
PDMF
pString
Sequencing Analysis Mobility file name chosen in collection
Peak
short[]
The peak dye indices
Peak
int[]
The peak data points
Peak
int[]
The peak begin data points
Peak
int[]
The peak end data points
Peak
short[]
FWHM of peak
Peak
double[]
Corrected FWHM of peak
Peak
int[]
The peak heights
Peak
int[]
The peak begin heights
Peak
int[]
The peak end heights
Peak
10
int[]
The peak area (in data points)
Peak
11
double[]
The corrected peak area (in data points)
Peak
12
double[]
The peak positions (in bases)
Peak
13
double[]
The peak begin positions (in bases)
Peak
14
double[]
The peak end positions (in base)
Peak
15
double[]
FWHM (in base) of peak
Peak
16
double[]
Corrected FWHM (in base) of peak
41
Name
Number
ABIF Type
Description
Peak
17
double[]
The peak area (in base)
Peak
18
double[]
The corrected peak area (in base)
Peak
19
cString
The peak labels separated by comma
Peak
20
cString
The flag indicating whether peak is size matched separated by comma
Peak
21
double[]
The base when peak is size matched
Peak
22
cString
The flag indicating whether peak is off-scale separated by comma
Peak
23
cString
The flag indicating whether peak is user created separated by comma
Peak
24
cString
The flag indicating whether peak is broaded
Peak
25
cString
The flag indicating whether peak is pullup
PSZE
long
Plate size. The number of sample positions in the container. Current

allowed values: 96, 384.
PTYP
cString
Plate type. Current allowed values: 96-Well, 384-Well.
PXLB
long
Pixel bin size. Currently limited to values of either 1 or 3.
Rate
User type
Scanning Rate. Milliseconds per frame.
RGCm
cString
Results Group comment. Not used for 3500. Reserved to preserve

backward compatibility.
RGNm
cString
Results Group name
RGOw
cString
The name entered as the Owner of a Results Group, in the Results Group
Editor. Implemented as the user name from the results group.
RInj
long
Reinjection number. The reinjection number that this sample belongs to.
Not present if there was no reinjection.
RNmF
float
Raman normalization factor
RMdN
cString
Module Name. This is redundant with MODF
RMdV
cString
Run Module Version
RMdX
char[]
Run Module XML String
RMXV
cString
Run Module XML Schema Version
RPrN
cString
Run Protocol Name
RPrV
cString
Run Protocol Version
RUND
date
Run Started Date
RUNT
time
Run Started Time
RUND
date
Run Stopped Date
RUNT
time
Run Stopped Time
RUND
date
Data Collection Started Date
RUNT
time
Data Collection Started Time
RUND
date
Data Collection Stopped date
RUNT
time
Data Collection Stopped Time
RunN
cString
Run name (which, for 3500, is different from injection name)
SamQ
cString
Quality values in key/value pair separated by comma
Satd
long[]
List of scan indexes which were saturated in the camera.
Scal
float
Rescaling Divisor for reducing the dynamic range of the color data.
42
Name
Number
ABIF Type
Description
SCAN
long
Number of scans. Redundant with Scan, but higher range.
Scan
short
Number of scans. Redundant with SCAN, but lower range. (legacy)
ScPa
cString
The parameter string of size caller
ScSt
long
Raw data start point. Set to 0 for 3500.data collection.
SnpS
pString
Snip set Name (optional)
SMAP
int[]
Scan numbers in size calling
SMAP
double[]
Base pairs in size calling
SMED
pString
Separation Medium Lot Exp Date
SMID
cString
Polymer first installed date
SMLt
pString
Separation Medium Lot Number (polymer lot number)
Sm#P
int
Number of size matched peaks
SMPL
pString
Sample information string. Same as STYP for 3500
SMRn
long
Number of runs (injections) processed with the current polymer (runs

allowed - runs remaining)
SpeN
cString
Active spectral calibration name
SpNm
pString
Fragment analysis Sample name
StdF
pString
Size Standard Name (from secondary analysis if it's available, otherwise

from primary analysis)
STYP
cString
Sample Type (alleleic ladder, sample, control, etc.)
SVER
pString
Data Collection version number
SVER
cString
Sizecaller version
SVER
pString
Firmware version number
SVER
pString
Sample File Format Version String
SzFt
double[]
Size match fitting parameters
SzFt
double
Size match R-Value
SZTS
cString
Time of completion of most recent analysis
Tmpr
long
Oven Temperature setting in degrees C
TUBE
pString
Autosampler position (A1-H1) (CapEP only)
UDEF
1-10
cString
User Defined names (optional)
User
pString
The name of the plate creator
UsrE
boolean
The flag indicating whether size match results have been edited by the
user. Unused for 3500. Reserved for backward compatibility.
43
Applied Biosystems 3730/3730xl DNA Analyzer tags

Software v2.0 on the Applied Biosystems 3730/3730xl DNA Analyzer (page 47)
Software v3.0 on the Applied Biosystems 3730/3730xl DNA Analyzer DNA
Analyzer (page 50)
Software v3.0 on the Applied Biosystems 3730/3730xl DNA Analyzer (page 53)
Name
Number
ABIF Type
APFN
pString
APXV
cString
APrN
cString
APrV
cString
APrX
char
BufT
short
Buffer tray heater temperature (degrees C)
CMNT
pString
CTID
cString
CTNM
cString
CTTL
pString
Comment title
CpEP
char
DATA
short
Channel 1 raw data
DATA
short
Channel 2 raw data
DATA
short
Channel 3 raw data
DATA
short
Channel 4 raw data
DATA
short
DATA
short
DATA
short
DATA
short
DSam
short
Downsampling factor
DySN
pString
44
Description
Dye set name
Name
Number
ABIF Type
Description
Dye#
short
DyeN
pString
Dye 1 name
DyeN
pString
Dye 2 name
DyeN
pString
Dye 3 name
DyeN
pString
Dye 4 name
DyeW
short
Dye 1 wavelength
DyeW
short
Dye 2 wavelength
DyeW
short
Dye 3 wavelength
DyeW
short
Dye 4 wavelength
EPVt
long
EVNT
pString
Start Run event
EVNT
pString
Stop Run event
EVNT
pString
EVNT
pString
FWO_
char
GTyp
pString
InSc
long
InVt
long
LANE
short
Lane/Capillary
LIMS
pString
Sample tracking ID
LNTD
short
Length to detector
LsrP
long
MCHN
pString
MODF
pString
MODL
char
Model number
NAVG
short
NLNE
short
OfSc
long
OvrI
1-N
long
PDMF
pString
PXLB
long
RGCm
cString
RGNm
cString
Results group name
RMXV
cString
Number of dyes
Base order

Pixel bin size
45
Name
Number
ABIF Type
RMdN
cString
RMdV
cString
Run Module version
RMdX
char
RPrN
cString
Run Protocol name
RPrV
cString
RUND
date
Run start date
RUND
date
Run stop date
RUND
date
RUND
date
RUNT
time
Run start time
RUNT
time
Run stop time
RUNT
time
RUNT
time
Rate
user
Scan rate.
RunN
cString
Run Name
SCAN
long
SMED
pString
SMLt
pString
Polymer lot number
SMPL
pString
Sample name
SVER
pString
SVER
pString
Satd
long
Scal
float
Scan
short
TUBE
pString
Tmpr
long
User
pString
46
Description
Number of scans
Well ID
Software v2.0 on the Applied Biosystems 3730/3730xl DNA Analyzer
Name
Number
ABIF Type
ANME
cString
BufT
short
1-N
pString
CTID
cString
CTNM
cString
CTTL
pString
Comment title
CpEP
char
DATA
short
Channel 1 raw data
DATA
short
Channel 2 raw data
DATA
short
Channel 3 raw data
DATA
short
Channel 4 raw data
DATA
short
DATA
short
DATA
short
DATA
short
DATA
105
short
DSam
short
Downsampling factor
DySN
pString
Dye#
short
Number of dyes
DyeB
char
DyeB
char
DyeB
char
DyeB
char
DyeB
char
DyeN
pString
Dye 1 name
DyeN
pString
Dye 2 name
DyeN
pString
Dye 3 name
DyeN
pString
Dye 4 name
DyeN
pString
Dye 5 name
DyeW
short
Dye 1 wavelength
DyeW
short
Dye 2 wavelength
DyeW
short
Dye 3 wavelength
DyeW
short
Dye 4 wavelength
CMNT
Description
GeneMapper software analysis method name
Dye set name
47
Name
Number
ABIF Type
DyeW
short
EPVt
long
EVNT
pString
Start Run event
EVNT
pString
Stop Run event
EVNT
pString
EVNT
pString
GTyp
pString
InSc
long
InVt
long
LANE
short
Lane/Capillary
LIMS
pString
Sample tracking ID
LNTD
short
Length to detector
LsrP
long
MCHN
pString
MODF
pString
MODL
char
Model number
NAVG
short
NLNE
short
OfSc
long
OvrI
1-N
long
OvrV
1-N
long
tags. (optional)
PANL
cString
PXLB
long
RGCm
cString
RGNm
cString
Results group name
RMXV
cString
RMdN
cString
RMdV
cString
Run Module version
RMdX
char
RPrN
cString
Run Protocol name
RPrV
cString
RUND
date
Run start date
RUND
date
Run stop date
48
Description

Pixel bin size
Name
Number
ABIF Type
Description
RUND
date
RUND
date
RUNT
time
Run start time
RUNT
time
Run stop time
RUNT
time
RUNT
time
Rate
user
Scan rate.
RunN
cString
Run Name
SCAN
long
SMED
pString
SMLt
pString
Polymer lot number
STYP
cString
GeneMapper software Sample Type
SVER
pString
SVER
pString
SVER
pString
Satd
long
Scal
float
Scan
short
SpNm
pString
StdF
pString
TUBE
pString
Well ID
Tmpr
long
User
pString
Number of scans

49
Software v3.0 on the Applied Biosystems 3730/3730xl DNA Analyzer DNA
Analyzer
Name
Number
ABIF Type
APFN
pString
APXV
cString
APrN
cString
APrV
cString
APrX
char
BufT
short
CMNT
pString
CTID
cString
CTNM
cString
CTOw
cString
Container owner
CTTL
pString
Comment title
CpEP
char
DATA
short
Channel 1 raw data
DATA
short
Channel 2 raw data
DATA
short
Channel 3 raw data
DATA
short
Channel 4 raw data
DATA
short
DATA
short
DATA
short
DATA
short
DATA
105
short
DCHT
short
DSam
short
Downsampling factor
DySN
pString
Dye#
short
DyeN
pString
Dye 1 name
DyeN
pString
Dye 2 name
DyeN
pString
Dye 3 name
DyeN
pString
Dye 4 name
DyeW
short
Dye 1 wavelength
DyeW
short
Dye 2 wavelength
DyeW
short
Dye 3 wavelength
50
Description
Dye set name

Number of dyes
Name
Number
ABIF Type
Description
DyeW
short
Dye 4 wavelength
EPVt
long
EVNT
pString
Start Run event
EVNT
pString
Stop Run event
EVNT
pString
EVNT
pString
FWO_
char
GTyp
pString
HCFG
cString
Instrument Class
HCFG
cString
Instrument Family
HCFG
cString
HCFG
cString
InSc
long
InVt
long
LANE
short
Lane/Capillary
LIMS
pString
Sample tracking ID
LNTD
short
Length to detector
LsrP
long
MCHN
pString
MODF
pString
MODL
char
Model number
NAVG
short
NLNE
short
OfSc
long
OvrI
1-N
long
OvrV
1-N
long
tags. (optional)
PDMF
pString
PSZE
long
PTYP
cString
PXLB
long
RGCm
cString
RGNm
cString
Results group name
Base order

values 96 and 384
Pixel bin size
51
Name
Number
ABIF Type
RMXV
cString
RMdN
cString
RMdV
cString
Run Module version
RMdX
char
RPrN
cString
Run Protocol name
RPrV
cString
RUND
date
Run start date
RUND
date
Run stop date
RUND
date
RUND
date
RUNT
time
Run start time
RUNT
time
Run stop time
RUNT
time
RUNT
time
Rate
user
Scan rate.
RunN
cString
Run Name
SCAN
long
SMED
pString
SMLt
pString
Polymer lot number
SMPL
pString
Sample name
SVER
pString
SVER
pString
Satd
long
Scal
float
Scan
short
TUBE
pString
Tmpr
long
User
pString
52
Description
Number of scans
Well ID
Software v3.0 on the Applied Biosystems 3730/3730xl DNA Analyzer
Name
Number
ABIF Type
ANME
cString
BufT
short
1-N
pString
CTID
cString
Container identifier, aka. plate barcode
CTNM
cString
CTOw
cString
Container owner
CTTL
pString
Comment title
CpEP
char
DATA
short
Channel 1 raw data
DATA
short
Channel 2 raw data
DATA
short
Channel 3 raw data
DATA
short
Channel 4 raw data
DATA
short
DATA
short
DATA
short
DATA
short
DATA
105
short
DCHT
short
DSam
short
Downsampling factor
DySN
pString
Dye#
short
Number of dyes
DyeB
char
DyeB
char
DyeB
char
DyeB
char
DyeB
char
DyeN
pString
Dye 1 name
DyeN
pString
Dye 2 name
DyeN
pString
Dye 3 name
DyeN
pString
Dye 4 name
DyeN
pString
DyeW
short
Dye 1 wavelength
DyeW
short
Dye 2 wavelength
CMNT
Description
GeneMapper analysis method name
Dye set name
53
Name
Number
ABIF Type
DyeW
short
Dye 3 wavelength
DyeW
short
Dye 4 wavelength
DyeW
short
EPVt
long
EVNT
pString
Start Run event
EVNT
pString
Stop Run event
EVNT
pString
EVNT
pString
GTyp
pString
HCFG
cString
Instrument Class
HCFG
cString
Instrument Family
HCFG
cString
HCFG
cString
InSc
long
InVt
long
LANE
short
Lane/Capillary
LIMS
pString
Sample tracking ID
LNTD
short
Length to detector
LsrP
long
MCHN
pString
MODF
pString
MODL
char
Model number
NAVG
short
NLNE
short
OfSc
long
OvrI
1-N
long
OvrV
1-N
long
tags. (optional)
PANL
cString
PSZE
long
PTYP
cString
PXLB
long
RGCm
cString
54
Description
GeneMapper panel name

values 96 and 384
Pixel bin size
Name
Number
ABIF Type
Description
RGNm
cString
Results group name
RMXV
cString
RMdN
cString
RMdV
cString
Run Module version
RMdX
char
RPrN
cString
Run Protocol name
RPrV
cString
RUND
date
Run start date
RUND
date
Run stop date
RUND
date
RUND
date
RUNT
time
Run start time
RUNT
time
Run stop time
RUNT
time
RUNT
time
Rate
user
Scan rate.
RunN
cString
Run Name
SCAN
long
SMED
pString
SMLt
pString
Polymer lot number
STYP
cString
GeneMapper Sample Type
SVER
pString
SVER
pString
SVER
pString
Satd
long
Array of longs representing the scan numbers of data points which are
Scal
float
Scan
short
SpNm
pString
Sample name for Genescan sample files
StdF
pString
TUBE
pString
Well ID
Tmpr
long
User
pString
Number of scans

55
2009 Life Technologies Corporation. All rights reserved.
For Research Use Only. Not for use in diagnostic procedures.
Information in this document is subject to change without notice. Applied Biosystems assumes no
responsibility for any errors that may appear in this document.
APPLIED BIOSYSTEMS DISCLAIMS ALL WARRANTIES WITH RESPECT TO THIS DOCUMENT,

EXPRESSED OR IMPLIED, INCLUDING BUT NOT LIMITED TO THOSE OF MERCHANTABILITY OR
FITNESS FOR A PARTICULAR PURPOSE. IN NO EVENT SHALL APPLIED BIOSYSTEMS BE LIABLE,
WHETHER IN CONTRACT, TORT, WARRANTY, OR UNDER ANY STATUTE OR ON ANY OTHER
BASIS FOR SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE OR CONSEQUENTIAL
DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT, INCLUDING BUT NOT
LIMITED TO THE USE THEREOF.
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09/2009

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Applied Biosystems Genetic Analysis

Data File Format

ABIF File Format Specification and Sample File Schema

ABIF File Format Specification and Sample File Schema

Applied Biosystems Genetic Analysis Data File Format

A note about support

ABIF File Format Specification and Sample File Schema

Important notes about compatibility

Important notes about compatibility

ABIF File Format Specification and Sample File Schema

Applied Biosystems Genetic Analysis Data File Format

The ABIF file format

ABIF File Format Specification and Sample File Schema

Overview of the ABIF format

Overview of the ABIF format

ABIF File Format Specification and Sample File Schema

Applied Biosystems Genetic Analysis Data File Format

ABIF File Format Specification and Sample File Schema

Detailed structure of the ABIF file

Detailed structure of the ABIF file

The header is a 128-byte area at the beginning of the file.

ABIF File Format Specification and Sample File Schema

Applied Biosystems Genetic Analysis Data File Format

//element type code

//size in bytes of one element

//number of elements in item

//size in bytes of item

//item's data, or offset in file

ABIF File Format Specification and Sample File Schema

The DirEntry Structure is shown schematically below.

therefore datasize may be larger than numelements x elementsize.

ABIF File Format Specification and Sample File Schema

Applied Biosystems Genetic Analysis Data File Format

directory offset + 28 x (N-1)

Each 28-byte entry consists of the following fields:

SInt32 name; // tag name

ABIF File Format Specification and Sample File Schema

SInt32 number; // tag number

SInt16 elementtype; // element type code

SInt16 elementsize; // size in bytes of one element

ABIF File Format Specification and Sample File Schema

Applied Biosystems Genetic Analysis Data File Format

SInt32 numelements; // number of elements in item

SInt32 datasize; // size in bytes of item

SInt32 dataoffset; // item's data, or offset infile

one byte with value

two character pString "AB"

array of two shorts {1, 2}

SInt32 datahandle; // reserved

ABIF File Format Specification and Sample File Schema

Unsigned 8-bit integer.

8-bit ASCII character or signed 8-bit integer

Unsigned 16-bit integer.

Signed 16-bit integer.

Signed 32-bit integer.

ABIF File Format Specification and Sample File Schema

Applied Biosystems Genetic Analysis Data File Format

32-bit floating point value.

64-bit floating point value.

Packed structure to represent calendar date: