Explanation of Records

Record

AC, ACcession line

Format

AC string

Explanation

A unique identifier for the reading.

Record

AP, Assembly Position

Format

AP Name_of_anchor_reading sense offset tolerance

Explanation

For readings whose position has been mapped by an external program, these records tell the "directed assembly" algorithm where to assemble the data. Positions are defined as offsets from an "anchor reading" which is the name of any reading already in the database, an orientation (sense, + or -), and a tolerance. Readings are aligned at relative position offset + or - tolerance.

Record

AQ, Average Quality of the reading.

Format

AQ Numeric value in range 1 - 99.

Explanation

The average value of the "numerical estimate of base calling accuracy" as calculated by program eba. The value is useful for monitoring data quality and could also be used for deciding on an order of assembly - for example assemble the highest quality readings first.

Record

AV, Accuracy Values

Format

AV q1 q2 q3 ... or a1,c1,g1,t1 a2,c2,g2,t2 ...

Explanation

The accuracy values lie in the range 1-99. Either 1 per base (eg 89 50 ... or 4 per base (eg 0,89,5,2 50,3,7,10). Bonfield,J.K and Staden,R. The application of numerical estimates of base calling accuracy to DNA sequencing projects. Nucleic Acids Res. 23 1406-1410, (1995).

Record

BC, Base Calling software

Record

CC, Comment line

Format

CC string

Explanation

Any comments can be added on any number of lines.

Record

CF, Cloning vector sequence File

Format

CF string

Explanation

The name of the file containing the sequence of the cloning vector, to be used by vector_clip (see section Screening Against Vector Sequences).

Record

CH, Special CHemistry

Format

CH number

Explanation

Used to flag readings as having been sequenced using a "special chemistry". The number is a bit pattern with a bit for each chemistry type, thus allowing combinations of chemistries to be listed. Currently bit 0 is used to distinguish between dye-primer (0) and dye-terminator (1) chemistries. Bits 1 to 4 inclusive indicate the type of chemistry: unknown (0, 0000), ABI Rhodamine (1, 0001), ABI dRhodamine (2, 0010), BigDye (3, 0011), Energy Transfer (4, 0100) and LiCor (5, 0101). So for example a BigDye Terminator has bits 00111 set which is 7 in decimal.

Record

CL, Cloning vector Left end

Format

CL number

Explanation

The base position in the sequence that contains the last base in the cloning vector. Currently gap4 only uses the CS line.

Record

CN, Clone Name

Format

CN string

Explanation

The name of the segment of DNA that the reading has been derived from. Typically the name of a physical map clone.

Record

CR, Cloning vector Right end

Format

CR number

Explanation

The base position in the sequence that contains the first base in the cloning vector. Currently gap4 only uses the CS line.

Record

CS, Cloning vector Sequence present in sequence

Format

CS range

Explanation

Regions of sequence found by vector_clip (see section Screening Against Vector Sequences) to be cloning vector. Used in assembly to exclude unwanted sequence.

Record

CV, Cloning Vector type

Format

CV string

Explanation

The type of the cloning vector used.

Record

DR, Direction of Read

Format

DR direction

Explanation

Whether forward or reverse primers were used. Allows mapping of forward and reverse reads off the same template. NOTE however that we do not encourage the use of this method as the terms direction, sense and strand can be confusing. Instead we encourage the use of the PRimer line.

Record

DT, DaTe of experiment

Format

DT dd-mon-yyyy

Explanation

Any date information.

Record

EN, Entry Name

Format

EN string

Explanation

The name given to the reading

Record

EX, EXperimental notes

Format

EX string

Explanation

Another type of comment line for additional information.

Record

FM, sequencing vector Fragmentation Method

Format

FM string

Explanation

Fragmentation method used to create sequencing library.

Record

ID, IDentifier

Format

ID string

Explanation

This is the name given to the reading inside the assembly database and is equivalent to the ID line of an EMBL entry.

Record

LE, Can be used to identify the location of materials

Format

LE string

Explanation

Originally a micro titre dish well number. Used in combination with LI.

Record

LI, Can be used to identify the location of materials

Format

LI string

Explanation

Originally a micro titre dish identifier. Used in combination with LE.

Record

LN, Local format trace file Name

Format

LN string

Explanation

The name of the local format trace file. This information is passed onto gap4, and allows for local formats to be used.

Record

LT, Local format trace file Type

Format

LT string

Explanation

The type of the local trace file type (usually SCF).

Record

MC, MaChine on which sequencing experiment was run

Format

MC string

Explanation

The lab's name for the sequencing machine used to create the data. Used for logging the performance of individual machines.

Record

MN, Machine generated trace file Name

Format

MN string

Explanation

The name of the trace file generated by the sequencing machine MC.

Record

MT, Machine generated trace file Type

Format

MT string

Explanation

The type of machine generated trace file.

Record

ON, Original base Numbers (positions)

Format

ON (eg) 1..43 0 45..63 65..74 0 75..536

Explanation

The A..B notation means that values A to B inclusive, so this example reads that bases 1 to 43 are unchanged, there is a change at 44, etc.

Record

OP, OPerator

Format

OP string

Explanation

Someone's name, possibly the person who ran the sequencing machine. Useful, with expansion of the string field for monitoring the performance of individuals!

Record

PC, Position in Contig

Format

PC number

Explanation

For preassembled data, the position to put the left end of the reading.

Record

PD, Primer Data

Format

PD sequence

Explanation

The primer sequence.

Record

PN, Primer Name

Format

PN string

Explanation

Name of primer used, using local naming convention. Could be a universal primer.

Record

PR, PRimer type

Format

PR number

Explanation

This record shows the direction of the reading and distinguishes between primers from the ends of the insert and those that are internal. It is important for the analysis of the relative orientations and positions of readings on templates. When the positions of readings on templates are analysed (see section Find read pairs) primer types 1,2,3 and 4 are represented using the symbols F,R,f and r respectively.

0

Unknown

1

Forward from beginning of insert

2

Reverse from end of insert

3

Custom forward i.e. a forward primer other than type 1.

4

Custom reverse i.e. a reverse primer other than type 2.

Record

PS, Processing Status

Format

PS explanation

Explanation

Indication of processing status.

Record

QL, poor Quality sequence present at Left (5') end

Format

QL position

Explanation

The sequence up to and including the base at the marked position are considered to be of too poor quality to be used. It may overlap with other marked sequences - CS, SL or SR. Used in assembly to exclude unwanted sequence.

Record

QR, poor Quality sequence present at Right (3') end

Format

QR position

Explanation

The sequence from and including the base at the marked position to the end is considered to be of too poor quality to be used. It may overlap with other marked sequences - CS, SL or SR. Used in assembly to exclude unwanted sequence.

Record

RS, Reference Sequence

Format

RS string

Explanation

The name of a sequence, usually in EMBL format, used to define the target sequence, base numbering and feature table data for a project. Used to define the numbering and changes produced by mutations in individual sequence readings (see section Introduction to mutation detection).

Record

SC, Sequencing vector Cloning site

Format

SC position

Explanation

The cloning site of the sequence vector. Used by vector_clip (see section Screening Against Vector Sequences).

Record

SE, SEnse (ie whether complemented)

Format

SE number

Explanation

For preassembled data, the sense of the reading (0 for forward, 1 for reverse).

Record

SF, Sequencing vector sequence File

Format

SF string

Explanation

The name of the file containing the sequence of the sequencing vector, to be used by vector_clip (see section Screening Against Vector Sequences).

Record

SI, Sequencing vector Insertion length

Format

SI range

Explanation

Expected insertion length of sequence in sequencing vector. Useful for selecting templates for further experiments.

Record

SL, Sequencing vector sequence present at Left (5') end

Format

SL position

Explanation

The sequence up to and including the base at the marked position are considered to be sequencing vector. Written by vector_clip (see section Screening Against Vector Sequences).

Record

SP, Sequencing vector Primer site (relative to cloning site)

Format

SP position

Explanation

Location of the primer using to sequence relative to cloning site. Used by vector_clip (see section Screening Against Vector Sequences).

Record

SQ, SeQuence

Format

SQ \nsequence blocks...\n//\n

Explanation

Complete sequence, as determined by the sequencing machine. The sequence is broken into blocks of 10 bases with 6 blocks per line separated by a space (see the example below).

Record

SR, Sequencing vector sequence present at Right (3') end

Format

SR position

Explanation

The sequence from and including the base at the marked position to the end are considered to be sequencing vector. Written by vector_clip (see section Screening Against Vector Sequences).

Record

SS, Screening Sequence

Format

SS string

Explanation

Note that in earlier versions of this documentation this field was explained incorrectly. Due to this the field is not currently being used by any of our programs. The original meaning was to specify a sequence to screen against. Any number of SS lines could be present to denote any number of screening sequences. In the future we may change the meaning of this field to be a single SS line containing a file of filenames of screening sequences. If this causes problems for people then we will choose a new line type, so please inform us now. Also note that contrary to previous documentation, vector_clip does not use this field (it uses the SF field instead).

Record

ST, STrands

Format

ST number

Explanation

Denotes whether this is a single or double stranded template. This is useful for deducing suitable templates for later experiments.

Record

SV, Sequencing Vector type

Format

SV string

Explanation

Type of sequencing vector used. Can be used for choosing templates for custom primer experiments.

Record

TC, Tag to be placed on the Consensus.

Format

TC TYPE S position..length

Explanation

These lines instruct gap4 to place tags on the consensus. The format defines the tag type which is a 4 character identifier and should start at column position 5), its strand ( "+", "-" or "=" which means both strands), its start position followed by the position of its end. These two values are separated by "..". Following lines starting TG with space characters up to column 10 are written into the comment field of the tag. For example the next three lines define a tag of type comment that is to be on both strands over the range 100 to 110 and the comment field will contain "This comment contains several lines".

TC   COMM = 100..110
TC        This comment contains
TC          several lines

Record

TG, Tag to be placed on the reading.

Format

TG TYPE S position..length

Explanation

These lines instruct gap4 to place tags on the reading. See TC for further information.

Record

TN, Template Name

Format

TN string

Explanation

The name of the template used in the experiment.

Record

WT, Wild Type trace file

Format

WT string

Explanation

The filename of the wild type trace file. Used for mutation studies.