The Caenorhabditis japonica genome was sequenced to a depth of 9X.
Approximately 6x coverage coming from plasmid and fosmid reads and
approximately 3x from 454 reads.  Source DNA was extracted from a
mixed population of females and males from all developmental stages.
The expected genome size is 166 Mb.  The whole-genome shotgun plasmid,
fosmid paired end reads and 454 reads were assembled using PCAP (Genome
Res. 13(9):2164-70 2003). 

Caenorhabditis japonica is described by Kiontke, Hironaka & Sudhaus
(Nematology 4:933-941, 2002) and the strain sequence is DF5081. This
strain was derived from the wild isolate DF5080. It was inbred by
Karin Kiontke in the laboratory of David Fitch for 20 generations by
transferring one young plugged gravid female per generation. It is
likely that this female had mated with only one of her brothers. The
strain DF5080 was established with 20 individuals collected from a
dead shield bug Parastrachia japonensis in Takeo, Japan by Toyoshi
Yoshiga. Takeo is 30 km away from Hinokuma Mountain Prefectural Park,
the locus typicus of C. japonica.

For answers to questions about this assembly or project, or any other
GSC genome project, please visit our Genome Groups web page
(http://genome.wustl.edu/genome_group_index.cgi) and email the
designated contact person.

Funding for the sequence characterization of this genome was provided 
by the National Human Genome Research Institute (NHGRI), National 
Institutes of Health (NIH).

'removed_data.fa.gz' in the output directory contains contigs <2kb and 
suspected contaminant contigs that have been removed from the assembly 
(contigs.fa/.qual and supercontigs.fa)

*** Contiguity: Contig ***
Total contig number: 103314
Total contig bases: 178330371 bp
Total Q20 bases: 174407234 bp
Q20 bases %: 97.8%
Average contig length: 1726 bp
Maximum contig length: 82650 bp
N50 contig length: 2842 bp
N50 contig number: 12519

Major contig (> 2000 bp) number: 21210
Major_contig bases: 109971014 bp
Major_contig Q20 bases: 109217057 bp
Major_contig Q20 base percent: 99.3%

Top tier (up to 100000000 bp): 
  Contig number: 16734
  Average length: 5976 bp
  Longest length: 82650 bp
  Contig bases in this tier: 100001719 bp
  Q20 bases in this tier: 99411378 bp
  Q20 base percentage: 99.4%
  Top tier N50 contig length: 7365 bp
  Top tier N50 contig number: 3993

Middle tier (100000000 bp -- 140000000 bp): 
  Contig number: 25355
  Average length: 1578 bp
  Longest length: 2439 bp
  Contig bases in this tier: 40000254 bp
  Q20 bases in this tier: 38849455 bp
  Q20 base percentage: 97.1%
  Middle tier N50 contig length: 1608 bp
  Middle tier N50 contig number: 10075

Bottom tier (140000000 bp -- end): 
  Contig number: 61225
  Average length: 626 bp
  Longest length: 1084 bp
  Contig bases in this tier: 38328398 bp
  Q20 bases in this tier: 36146401 bp
  Q20 base percentage: 94.3%
  Bottom tier N50 contig length: 753 bp
  Bottom tier N50 contig number: 21398



*** Contiguity: Supercontig ***
Total supercontig number: 73122
Average supercontig length: 2439 bp
Maximum supercontig length: 899118 bp
N50 supercontig length: 35550 bp
N50 supercontig number: 900

Major supercontig (> 2000 bp) number: 8217
Major_supercontig bases: 131306720 bp
Major_supercontig Q20 bases: 130000972 bp
Major_supercontig Q20 base percent: 99%

Scaffolds > 1M: 0
Scaffold 250K--1M: 43
Scaffold 100K--250K: 240
Scaffold 10--100K: 1753
Scaffold 5--10K: 825
Scaffold 2--5K: 5351
Scaffold 0--2K: 64910

Top tier (up to 100000000 bp): 
  Supercontig number: 1293
  Average length: 77349 bp
  Longest length: 899118 bp
  Contig bases in this tier: 100011858 bp
  Q20 bases in this tier: 99207184 bp
  Q20 base percentage: 99.1%
  Top tier N50 supercontig length: 102494 bp
  Top tier N50 supercontig number: 263

Middle tier (100000000 bp -- 140000000 bp): 
  Supercontig number: 12622
  Average length: 3169 bp
  Longest length: 20799 bp
  Contig bases in this tier: 40000561 bp
  Q20 bases in this tier: 39147786 bp
  Q20 base percentage: 97.8%
  Middle tier N50 supercontig length: 3260 bp
  Middle tier N50 supercontig number: 2369

Bottom tier (140000000 bp -- end): 
  Supercontig number: 59207
  Average length: 647 bp
  Longest length: 1275 bp
  Contig bases in this tier: 38317952 bp
  Q20 bases in this tier: 36052264 bp
  Q20 base percentage: 94%
  Bottom tier N50 supercontig length: 774 bp
  Bottom tier N50 supercontig number: 19894