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  Non-Standard Join Certificates
  Occasionally, sequence joins between adjacent clones in the human genome reference sequence cannot be computationally validated because the clones originate from different haplotypes and contain polymorphisms in the overlapping sequence, or the overlap is too small to be to be reliable. In these instances, the sequencing center responsible for the particular chromosome has provided data to support the join in the form of an electronic certificate. These certificates are grouped by assembly version and stored in table format.

The remainder of this page describes the format and conventions used by the sequencing centers to generate the electronic certificates. To view the certificates for a specific assembly, click on one of the following links. For more information about a specific join, use the email address listed under the Contact column in the table.

  Certificate Formats and Conventions

Information contained on all certificates:

  • CONTACT: {email address}
  • DATE: {date}

Case 1: Blunt join, or short overlap (~ <30 bp) supported by GenBank sequence

  • JOIN {accession.version} {accession.version}
  • OVERLAP: {bp}
  • SPANNER: {accession.version}
  • COMMENT: {some text}
Case 2: Gaps in alignment due to polymorphism
  • JOIN {accession.version} {accession.version}
  • VARIATION TYPE: { LINE | SINE | SSLP | other }
  • VARIATION EVIDENCE: {short comment}
  • COMMENT: {some text}

Case 3: Catch-all for everything else

  • JOIN {accession.version} {accession.version}
  • OTHER EVIDENCE: {short comment}
  • COMMENT: {some text}

Conventions for submission and evaluation

Blunt/short joins should be resolved by reference to adequate overlapping sequence data by one of the following means:

  • submission to the database of additional finished overlap data from the flagged clones or from a new overlapping clone.
  • submission of a certificate indicating an overlapping portion of an unfinished accession that supports the join by overlap.
In general, providing a comment about any fosmid or BAC linking information is helpful. Excessive numbers of linking clones may be a cause for closer examination.

Questioned polymorphic joins should be resolved by submitting a certificate. For polymorphic joins, include the size of the polymorphic region (e.g. number of extra bases due to SSLP, etc.) and its location. For questioned joins due to SINE, LINE, or SSLP:

  • Support by BAC- or fosmid-end linking information in the certificate is sufficient to validate. No PCR or other analysis need be done unless the coordinator desires to. If there is only a single link, it may be worth erring on the side of caution. If there are multiple distinct problems of this type in one join, additional analyses should usually be done. If there appear to be excessive BAC or fosmid links, the certificate will be flagged for further discussion.
  • If there is no support from BAC or fosmid linking data, experimental support (e.g. PCR analysis of several individuals) should be obtained (and stated in certificate) to validate.
  • For questioned joins due to other types of polymorphisms (in/dels, inversions, etc.), a certificate is valid only if additional support (e.g. PCR) is provided beyond linking information.

General comments:

  • The information in the certificate should state why the submittor thinks the join is valid.
  • Certificates should include the length of overlap between clones.
  • BAC- and fosmid-end linking information is allowable as support and should be included in certificates.
  • Certificates should be submitted for questioned joins even if problems are not yet resolved. Comment should state "not yet resolved".
  • If a join has more than one problem, only one certificate should be submitted listing both problems. Generally, the more severe problem should be listed first. If the problems are of two different types (e.g. polymorphism and blunt join), the certificate category should be used for the more serious problem.


The evaluator will add the following to all certificates upon examination:

REMARK: {text}

with the following allowable "words":

  • Pass
  • Return (return to coordinator)
  • In process (this is for cases clearly being worked on in the right way but not yet resolved)
  • Disputed (for Return cases where there is not agreement after one round of back-and-forth)
  • Unresolved (this is a catch-all for any unresolved situation that is not in one of the above categories)