These are for use in the TEXT segments. None are required, but if any of these identifiers are present they must confirm to the description below. Much (currently all) of this list has been taken from the NCBI Trace Archive [2] documentation. It is duplicated here as the ZTR spec is not tied to the same revision schedules as the NCBI trace archive (although it is intended that any suitable updates to the trace archive should be mirrored in this ZTR spec).
The Trace Archive specifies a maximum length of values. The ZTR spec does not have length limitations, but for compatibility these sizes should still be observed.
The Trace Archive also states some identifiers are mandatory; these are marked by asterisks below. These identifiers are not mandatory in the ZTR spec (but clearly they need to exist if the data is to be submitted to the NCBI).
Finally, some fields are not appropriate for use in the ZTR spec, such as BASE_FILE (the name of a file containing the base calls). Such fields are included only for compatibility with the Trace Arhive. It is not expected that use of ZTR would allow for the base calls to be read from an external file instead of the ZTR BASE chunk.
[ Quoted from TraceArchiveRFC v1.17 ]
Identifier Size Meaning Example value(s)
---------- ----- ---------------------------- -----------------
TRACE_NAME * 250 name of the trace HBBBA1U2211
as used at the center
unique within the center
but not among centers.
SUBMISSION_TYPE * - type of submission
CENTER_NAME * 100 name of center BCM
CENTER_PROJECT 200 internal project name HBBB
used within the center
TRACE_FILE * 200 file name of the trace ./traces/TRACE001.scf
relative to the top of
the volume.
TRACE_FORMAT * 20 format of the tracefile
SOURCE_TYPE * - source of the read
INFO_FILE 200 file name of the info file
INFO_FILE_FORMAT 20
BASE_FILE 200 file name of the base calls
QUAL_FILE 200 file name of the base calls
TRACE_DIRECTION - direction of the read
TRACE_END - end of the template
PRIMER 200 primer sequence
PRIMER_CODE which primer was used
STRATEGY - sequencing strategy
TRACE_TYPE_CODE - purpose of trace
PROGRAM_ID 100 creator of trace file phred-0.990722.h
program-version
TEMPLATE_ID 20 used for read pairing HBBBA2211
CHEMISTRY_CODE - code of the chemistry (see below)
ITERATION - attempt/redo 1
(int 1 to 255)
CLIP_QUALITY_LEFT left clip of the read in bp due to quality
CLIP_QUALITY_RIGHT right " " " " "
CLIP_VECTOR_LEFT left clip of the read in bp due to vector
CLIP_VECTOR_RIGHT right " " " " "
SVECTOR_CODE 40 sequencing vector used (in table)
SVECTOR_ACCESSION 40 sequencing vector used (in table)
CVECTOR_CODE 40 clone vector used (in table)
CVECTOR_ACCESSION 40 clone vector used (in table)
INSERT_SIZE - expected size of insert 2000,10000
in base pairs (bp)
(int 1 to 2^32)
PLATE_ID 32 plate id at the center
WELL_ID well 1-384
SPECIES_CODE * - code for species
SUBSPECIES_ID 40 name of the subspecies
Is this the same as strain
CHROMOSOME 8 name of the chromosome ChrX, Chr01, Chr09
LIBRARY_ID 30 the source library of the clone
CLONE_ID 30 clone id RPCI11-1234
ACCESSION 30 NCBI accession number AC00001
PICK_GROUP_ID 30 an id to group traces picked
at the same time.
PREP_GROUP_ID 30 an id to group traces prepared
at the same time
RUN_MACHINE_ID 30 id of sequencing machine
RUN_MACHINE_TYPE 30 type/model of machine
RUN_LANE 30 lane or capillary of the trace
RUN_DATE - date of run
RUN_GROUP_ID 30 an identifier to group traces
run on the same machine
[ End of quote from TraceArchiveRFC ]
More detailed information on the format of these values should be obtained
from the Trace Archive RFC [2].