Clone List

List of clones in the rearray

Each clone is formatted using Genbank name convention (e.g. RP11-182G10) and fingerprint mapping convention (e.g. N0182G10). The second column contains the FPC database name, and the third column provides the FPC canonical name. The database name may contain prefixes and suffixes (7N0467H10bw) in the canonical name (N0467H10).

Clone Sequence Coordinates (Weak Hits)

Clones localized by fingerprint-based alignments (fingerprint profiling, fpp) have their strongest hit reported in the coordinate file. This auxiliary coordinate file lists all fingerprint-based alignments. The alignments include the alignment score.

Clone Sequence Coordinates (Details)

Comparison of fingerprint-based alignments (fpp) and end sequence alignments (bes) for clones for which both alignment types are available.

ab/af = fraction of bes/fpp alignment overlapping with fpp/bes alignment; dl/dr = distance between left/right ends of fpp and bes alignments; u = left/right ends of union of fpp and bes alignments; q = size(intersectino fpp and bes)/size(u); fpsize = total size of fingerprint fragments

Clone Sequence Coordinates

Assembly coordinate annotations for array clones. Precise sequence position is available for the vast majority of clones (>98%). Coordinates are determined by either end sequence alignments (bes), when available, or fingerprint-based alignments (fpp).

Clone Sequence Coordinates (Validation)

This file presents validation information showing the degree of corroboration of clone mappings in the fingerprint map and sequence. For each clone in the rearray, a 10-clone neighbourhood is selected from neighbouring canonical map clones with sequence coordinates. The union of sequence coordinates of these map clones from a set of neighbourhoods against which the clone's sequence position is compared.

The last field in this file reports the level of corroboration: "inside" indicates that the clone's sequence mapping is within its map-derived neighbourhood, "outside" indicates that the clone's position is on a different chromosome than suggested by its map-derived neighbourhood, "NUM" when the field is a number the clone is on the same chromosome as the neighbourhood, but not overlapping, and the number is the distance between the two positions, "none" indicates that the clone had no coordinate-bearing neighbours.

Clone Fingerprint Map Position

The rearray clones are selected primarily from the fingerprint map, with some replacement and gap-filling clones selected from the pool of sequenced and end-sequenced clones. This file provides position of rearray clones in the fingerprint map.

The fields in this file are: canonical mapping name, fpc mapping name, "alias" if the fpc mapping name is contains a prefix/suffix (usually indicates multiple fingerprints for a clone), genbank name, fingerprint map contig number, cbmap start/end position, canonical/buried status.

Clone Fingerprint Map Partition Covers

The entire fingerprint map is represented as a series of partitions generated from the cbmap overlap intervals of all clones in the map. Each partition has a size and is annotated by the number of map clones and array clones that intersect the partition. The partition covers are helpful in determining which clones provide coverage of specific cbmap intervals.

Clones are annotated by (v) when virtual, (B) when buried, (R) when in the rearray. Rearray clones also have their coordinates reported with "typeXXX:chrNN:posNNN-NNN".

Fingerprint Map Coverage

This file describes the coverage of the fingerprint map in terms of the representation of the cbmap unit scale by the clones in the array. Coverage of various elements in the fingerprint map (contig, all clones, canonical clones, buried clones, rearray clones, rejected clones, gaps, gaps by rejected clones) are annotated by the set of cbmap units (RUNLIST lines) that these elements cover as well as the total size of the set (CARDINALITY lines).

Overlap by Fingerprint

The relationship between array clones found adjacent in the fingerprint map is reported. The fingerprint similarity of each adjacent pair of clones can be related to the overlap of the clones.

nb, number of bands; cb, cbmap unit interval; intermedial, number of clones between the pair; enddiff, dbmap unit difference between the right ends of the clone; s, number of conserved fragments, ssize, size of conserved fragments; m, number of shared fragments; msize, size of shared fragments; -logZ, negative logarithm (base10) of the Sulston score

Array Plate Position

Location of each clone in the original BCGSC rearray plates. If you have obtained your rearray from BACPAC, you should use the chromosome-specific rearray plate mappings.

Array Plate Position (Chromosomal Rearray)

The clone array is available from BACPAC (bacpac.chori.org) in chromosome-specific plates (clones have been rearrayed at BACPAC according to their chromosomal assignments at the time of the rearray). The plate positions of the clones are availble from BACPAC. This file recapitulates this information. Empty wells are annotated by "empty" and "status 0" fields.