Background:

The chimpanzee genome (Pan troglodytes) genome was originally
sequenced to 4X coverage using a male captive born chimp of West
Africa origin known as "Clint" from the Yerkes Primate Research Center
(Atlanta, USA). The revised assembly (Pan_troglodytes-2.1) described
below represents an additional 2X whole genome shotgun plasmid reads
which were generated as part of our sequence improvement plan for the
existing 4X chimp assembly (Pan_troglodytes-1.0). As before, the
combined sequence reads were assembled using the PCAP software (Genome
Res. 13(9):2164-70 2003) and filtered for all known non-chimp sequence
contaminants. Finished chromosome 21 sequence data was kindly provided
by Todd Taylor and the Riken Genome Sciences Center (Watanabe et al.,
DNA sequence and comparative analysis of chimpanzee chromosome
22. Nature. 2004 May 27;429(6990):382-8. PMID: 15164055) to complete
chimp "Clint" chromosome 21 and the chromosome Y sequence was finished
at the Washington University Genome Sequencing Center with detailed
mapping and extensive collaboration with David Page's group at the
Whitehead Institute (The DNA Sequence of Chimpanzee Chromosome Y,
unpublished; Hughes et al., Conservation of Y-linked genes during
human evolution revealed by comparative sequencing in chimpanzee.
Nature, 2005 437:100-3; PMID: 16136134). Ongoing sequence improvement
efforts at WUGSC will act to further enhance this most recent 6X draft
assembly with the expectation that another improved assembly will be
available in the future. For questions regarding this chimp assembly
please visit our existing chimp genome web page and contact the
designated person for chimp. Downloads of the sequence data are
available via our genome browser FTP server. 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:

project: chimp_051011_2.1
total reads input: 34014260
total reads placed: 29898661
total reads unplaced: 4115599
chaff rate: 0.12

total input phred20 bases: 19699021002
estimated genome size: 3000000000
total contig length added sum: 3160935199
phred20 bases sequence redundance: 6.57 X
total input reads bases: 25812564886
average phred20 per read: 579.14
average read length: 758.87

Sequence assembly statistics:

total contig number: 505703
maximun contig length: 288547
major contig (> 1kb) number: 359644

total supercontig number: 275931
maximun supercontig length: 44063386
major supercontig (> 1kb) number: 146124

based on the added contigs sum
contig N50 length:26384, contig N50 number: 32093
supercontig N50 length:7679112, supercontig N50 number: 100

total GC counts in the genome: 1287378131 percentage: 0.41
total AT counts in the genome: 1873012645 percentage: 0.59
total NX counts in the genome: 544423


total mate pairs forward reverse constraints: 16387973
total unsatisfied constraints excluding due to singlton, short supercontig, and supercontigs end: 239522
total unsatisfied rate:  1.46 %


No. of satisfied constraints in contigs:     8810215
No. of unsatisfied in distance in contigs:    238737
No. of satisfied links in scaffolds:         3314497
No. of unsatisfied in dist. in scaffolds:     315304
No. of unsatisfied due to singlets:          2536945
No. of unsatisfied due to short scaffolds:    685377
No. of unsatisfied due to scaffold ends:       48880
No. of other unsatisfied constraints:         239522
No. of redundant constraints:                 198496
Total no. of satisfied constraints:         12124712
Total no. of unsatisfied constraints:        4064765
Total no. of constraints:                   16387973