Some Terminology
(FPC) Contig
  In this context means the largest scale of Golden Path structure below that of the Chromosome. This is a 'clone contig' or FPC, a group of clones associated by the WashU map. Groups of clones in a 'contig' are organized into barges, then laid out along the chromosome as a whole.
Barge
  a series of clones within an FPC contig that show sequence overlap and can be ordered linearly
raft
  a set of fragments from overlapping clones that is assembled by ooGreedy into a continuous stretch of sequence
fragment
  a sequence contig inside of an accessioned clone (BAC, PAC or cosmid). A fragment is assembled from reads usually by Phrap.
read
  a (typically 300-1000) base sequence that was produced by a single lane or capillary on a sequencing machine. (No assembly required).
Input
  Statistic is calculated on data before any assembly is done; all available data.
Pre-GP
  Statistic is calculated on Genome data before final distillation of the Assembly into the Golden Path. Thus, all overlapping sequence is included.
Golden Path / GP
  The Golden Path is the finished distillate of the assembly process. Unless otherwise stated, all statistics on this page can be assumed derived from Golden Path data.
Weighted Median
  For an object associated with a length in basepairs along the Golden Path (only), "The length such that half the basepairs in the overall sequence are in objects of the same type with equal or lesser length". This more algorithmically described as: for datapoints x[1..N] (in ascending order), x[k] for the first k such that the sum of x[i] for i less than k is greater than or equal to half the sum of all datapoints.
Weighted Mean
  An average over lengths, weighted proportionally to those lengths.
Bridged Clone Gap
  A gap between two barges which are known to be near one another, generally by mRNA or BAC-end hits. These are represented in the Golden Path as 50 Kb inserts of 'N's.
Unbridged Clone Gap
  A gap between two barges which have no evidence for adjacency. These are represented in the Golden Path as 100 Kb inserts of 'N's.
Size
  Here, size and extent have specific, and different, meaning. The 'Size' of a genomic object is the number of actual basepairs it includes - i.e., it doesn't include any gaps. So, for example, the 'size' of a clone is the sum of the lengths of its (nonoverlapping, for GP stats) fragments.
Extent
  How much space the object takes up on the genome - how far apart, in basepairs, its extreme points are.
Coverage
  How thoroughly an clone is sequenced - specifically, the ratio of the Size to the Extent.
Finished, Deep, Draft Rafts
  These are classifications fo Rafts:
  - Finished: raft contains at least one finished clone fragment. Often abbrev. 'Fin'.
  - Deep: Unfinished raft that contains fragments from at least two different draft clones.
  - Draft: All other rafts