Web table description and disclaimer

Table description. This table provides all the currently available mapping and/or linking information on every scaffold that satisfies any of the following conditions:

- Nov. 2003 release scaffolds, either completely finished at TIGR (URL) or linked to telomeres at both ends (even if not finished);

- Nov. 2003 release scaffolds that have been linked to at least one more scaffold by HAPPY-mapping (mainly), coassortment or PCR amplification. The LOD (log of the odds) against linkage is shown for every link obtained by HAPPY mapping.

- Unlinked, open-ended scaffolds with available genetic map information.

Key to the web scaffold table.

Information in columns beyond the first two applies to the superscaffold to which the scaffold belongs.

nd (in any column) = not determined.

Superscaf id: temporary id for the superscaffold. Closed_xxxx means TIGR-finished scaffold, where xxxx is the TIGR identifier

Arm: MIC-chromosome arm. X means unidentified arm of chromosome 5.

Lkg: linkage group

Cag: coassortment group

Seq_loc and mapped_scaf: Locus in the genetic map related to the particular scaffold in the superscaffold

Chr_length: Length of the MAC chromosome carrying the sequenced locus as physically measured by hybridization. ~10% is the margin of error that we tolerate due to pulsed field gel electrophoresis resolution and thickness of the autoradiogram band.

Superscaf length: current length of the superscaf as determined by adding the lengths of the component scaffolds.

Pol_tag: whether or not any scaffold of the superscaffold carries a genetically mapped polymorphism

Capped_end: L and R: Telomere cap at the right (3’) and left (5’) ends of the assembly; N: neither end. LR: completely assembled MAC chromosome

Assembly: Assemblies or individual scaffolds. + = telomere cap; ++ = telomere caps in finished MAC chromosomes; numbers in square brackets: log of the odds (LODs) against independent segregation in the HAPPY mapping panel (see disclaimer below, which will accompany the table in the internet)

Disclaimer on the statistical reliability of HAPPY link LODs. The guiding principle has been to include in this table the most reliable information available, with the strong caveat that an unknown minority of the currently statistically less reliable link information will turn out to be incorrect when the assembly has been completed. Linkages experimentally confirmed (to be arbitrarily assigned LOD = PCR), and only those, can be trusted. LOD 5 links are virtually certain to be correct; while not every LOD 5 link has been experimentally tested, every one that has been tested has been confirmed. Below 5, the lower the LOD, the less the likelihood that the link is real. If the reality of a particular link is critical to your work, we urge you to consult with the Orias lab to find out if updated information has more recently become available or to seek advice on how best to proceed to check the linkage in question.