Raw sequence Individual unassembled sequence reads, produced by sequencing of clones containing DNA inserts.
Paired-end sequence Raw sequence obtained from both ends of a cloned insert in any vector, such as a plasmid or bacterial artificial chromosome.
Finished sequence Complete sequence of a clone or genome, with an accuracy of at least 99.99% and no gaps.
Coverage (or depth) The average number of times a nucleotide is represented by a high-quality base in a collection of random raw sequence. Operationally, a 'high-quality base' is defined as one with an accuracy of at least 99% (corresponding to a PHRED score of at least 20).
Full shotgun coverage The coverage in random raw sequence needed from a large-insert clone to ensure that it is ready for finishing; this varies among centres but is typically 8–10-fold. Clones with full shotgun coverage can usually be assembled with only a handful of gaps per 100 kb.
Half shotgun coverage Half the amount of full shotgun coverage (typically, 4–5-fold random coverage).
BAC clone Bacterial artificial chromosome vector carrying a genomic DNA insert, typically 100–200 kb. Most of the large-insert clones sequenced in the project were BAC clones.
Finished clone A large-insert clone that is entirely represented by finished sequence.
Full shotgun clone A large-insert clone for which full shotgun sequence has been produced.
Draft clone A large-insert clone for which roughly half-shotgun sequence has been produced. Operationally, the collection of draft clones produced by each centre was required to have an average coverage of fourfold for the entire set and a minimum coverage of threefold for each clone.
Predraft clone A large-insert clone for which some shotgun sequence is available, but which does not meet the standards for inclusion in the collection of draft clones.
Contigs and scaffolds
Contig The result of joining an overlapping collection of sequences or clones.
Scaffold The result of connecting contigs by linking information from paired-end reads from plasmids, paired-end reads from BACs, known messenger RNAs or other sources. The contigs in a scaffold are ordered and oriented with respect to one another.
Fingerprint clone contigs Contigs produced by joining clones inferred to overlap on the basis of their restriction digest fingerprints.
Sequenced-clone layout Assignment of sequenced clones to the physical map of fingerprint clone contigs.
Initial sequence contigs Contigs produced by merging overlapping sequence reads obtained from a single clone, in a process called sequence assembly.
Merged sequence contigs Contigs produced by taking the initial sequence contigs contained in overlapping clones and merging those found to overlap. These are also referred to simply as 'sequence contigs' where no confusion will result.
Sequence-contig scaffolds Scaffolds produced by connecting sequence contigs on the basis of linking information.
Sequenced-clone contigs Contigs produced by merging overlapping sequenced clones.
Sequenced-clone-contig scaffolds Scaffolds produced by joining sequenced-clone contigs on the basis of linking information.
Draft genome sequence The sequence produced by combining the information from the individual sequenced clones (by creating merged sequence contigs and then employing linking information to create scaffolds) and positioning the sequence along the physical map of the chromosomes.
N50 length A measure of the contig length (or scaffold length) containing a 'typical' nucleotide. Specifically, it is the maximum length L such that 50% of all nucleotides lie in contigs (or scaffolds) of size at least L.
Computer programs and databases
PHRED A widely used computer program that analyses raw sequence to produce a 'base call' with an associated 'quality score' for each position in the sequence. A PHRED quality score of X corresponds to an error probability of approximately 10-X/10. Thus, a PHRED quality score of 30 corresponds to 99.9% accuracy for the base call in the raw read.
PHRAP A widely used computer program that assembles raw sequence into sequence contigs and assigns to each position in the sequence an associated 'quality score', on the basis of the PHRED scores of the raw sequence reads. A PHRAP quality score of X corresponds to an error probability of approximately 10-X/10. Thus, a PHRAP quality score of 30 corresponds to 99.9% accuracy for a base in the assembled sequence.
GigAssembler A computer program developed during this project for merging the information from individual sequenced clones into a draft genome sequence.
Public sequence databases The three coordinated international sequence databases: GenBank, the EMBL data library and DDBJ.
STS Sequence tagged site, corresponding to a short (typically less than 500 bp) unique genomic locus for which a polymerase chain reaction assay has been developed.
EST Expressed sequence tag, obtained by performing a single raw sequence read from a random complementary DNA clone.
SSR Simple sequence repeat, a sequence consisting largely of a tandem repeat of a specific k-mer (such as (CA)15). Many SSRs are polymorphic and have been widely used in genetic mapping.
SNP Single nucleotide polymorphism, or a single nucleotide position in the genome sequence for which two or more alternative alleles are present at appreciable frequency (traditionally, at least 1%) in the human population.
Genetic map A genome map in which polymorphic loci are positioned relative to one another on the basis of the frequency with which they recombine during meiosis. The unit of distance is centimorgans (cM), denoting a 1% chance of recombination.
Radiation hybrid (RH) map A genome map in which STSs are positioned relative to one another on the basis of the frequency with which they are separated by radiation-induced breaks. The frequency is assayed by analysing a panel of human–hamster hybrid cell lines, each produced by lethally irradiating human cells and fusing them with recipient hamster cells such that each carries a collection of human chromosomal fragments. The unit of distance is centirays (cR), denoting a 1% chance of a break occuring between two loci.