Background:

The chimpanzee genome (Pan troglodytes) was sequenced to 4X coverage
using a West African male chimp known as "Clint" from the Yerkes
Primate Research Center (Atlanta, GA) in a collaboration with the
Broad Institute of the Massachusetts Institute of Technology and
Harvard University (Cambridge, MA) The genome sequencing strategy
employed plasmids, fosmids and BAC end sequences. The sequenced reads
were assembled using ARACHNE and PCAP (Genome Res. 13(9):2164-70
2003)assembly software tools. The assembly described here
(Pan_troglodytes-1.0) represents the PCAP version. This 4X PCAP
assembly was filtered for all known non-chimp sequence
contaminants. The ARACHNE assembly was used for the analysis that
appeared in the September 1, 2005 issue of Nature. Ongoing sequence
improvement efforts at WUGSC will act to further enhance this 4X draft
assembly. For questions regarding this chimp assembly please visit our
existing chimp genome web page and contact the designated person for
chimp. Funding for the sequence characterization of the chimp genome
was provided by the National Human Genome Research Institute (NHGRI),
National Institutes of Health (NIH).

Production Sequencing statistics:

Pan_troglodytes-1.0
total reads input: 21466717
total reads placed: 18728807
total reads unplaced: 2737910
chaff rate: 0.13


total input phred20 bases: 12486637483
estimated genome size: 3000000000
total contig length added sum: 2687769690
phred >20 bases sequence redundancy: 4.16 X
total input reads in bases: 17125154663
average phred >20 per read: 581.67
average base pair read length: 797.75

Sequence assembly statistics:

total contig number: 435593
maximum contig length: 144170
major contig (> 1kb) number: 400289

total supercontig number: 81459
maximum supercontig length: 11937040
major supercontig (> 1kb) number: 67734

based on the added contigs sum
contig N50 length:13096, contig N50 number: 58492
supercontig N50 length:2344823, supercontig N50 number: 308

total GC counts in the genome: 1095327134  percentage: 0.41
total AT counts in the genome: 1591983718  percentage: 0.59
total NX counts in the genome: 458838

The total repeats bases exceed threshold 50
is about 0.15 % of the total bases

total mate pairs forward reverse constraints: 10037101
total unsatisfied constraints excluding due to singleton, short supercontig, and supercontigs end: 89445
total unsatisfied rate:  0.89 %

No. of satisfied constraints in contigs:     4189805
No. of unsatisfied in distance in contigs:     21952
No. of satisfied links in scaffolds:         3249474
No. of unsatisfied in dist. in scaffolds:     152310
No. of unsatisfied due to singlets:          1724749
No. of unsatisfied due to short scaffolds:    524321
No. of unsatisfied due to scaffold ends:       31667
No. of other unsatisfied constraints:          89445
No. of redundant constraints:                  53378
Total no. of satisfied constraints:          7439279
Total no. of unsatisfied constraints:        2544444
Total no. of constraints:                   10037101