Sequencing Status Help

The Rice sequencing status Web Pages display information about clones that have GenBank entries (SD clones).

Nightly, updated and new sequenced clones are downloaded from GenBank.
A program that computes the simulated digest is run on each sequence, the SD (simulated digest) clone is entered into FPC, compared with all clones in FPC, and placed in the same location of its best hit.
Hence, SD refers to Genbank clones that have been entered into FPC.

Currently we have status pages for clones from rice and maize genomes.

Column Description
The following columns are displayed on the status page:

Chromsome: lists total number of chromosomes present in a genome. All clones that do not go into a contig are assigned to Chromosome 0.

# SD Clones: This column contains a count of the SD clones that have been entered into FPC.

# Finished: count of the number of clones that have been annotated as finished in the GenBank records.

# Repeats: count of the number of repeat regions in a given chrosome. This count is obtained by reading through GenBank records of each clone.

Total Size: summation of known clone lengths obtained from GenBank records. This value expressed in Mega Bases (Mb) is an approximate value, since it includes overlaps too.

Estimated Size: approximate known size of the entire chromsome in Mega Bases (Mb).