The Caenorhabditis japonica genome was sequenced to a depth of 6.3X
using plasmid and fosmid libraries made from DNA extracted from a
mixed population of females and males from all developmental stages.
The expected genome size is 83 Mb.  The whole-genome shotgun plasmid
and fosmid paired end reads were assembled using PCAP (Genome
Res. 13(9):2164-70 2003).  Additional coverage and primer-directed
sequence improvement are ongoing at the GSC.

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).

*** Contiguity: Contig ***
Total contig number: 35286
Total contig bases: 129372961 bp
Total Q20 bases: 124576772 bp
Q20 bases %: 96.2%
Average contig length: 3666 bp
Average major (> 2000 bp) contig length: 5501
Maximum contig length: 51942 bp
N50 contig length: 5781 bp
N50 contig number: 6367

Major contig (> 2000 bp) number: 20069
Major_contig bases: 110404923 bp
Major_contig Q20 bases: 107512353 bp
Major_contig Q20 base percent: 97.4%

Top tier (up to 90000000 bp):
  Contig number: 12132
  Average length: 7419 bp
  Longest length: 51942 bp
  Contig bases in this tier: 90002401 bp
  Q20 bases in this tier: 88256438 bp
  Q20 base percentage: 98%
  Top tier N50 contig length: 8258 bp
  Top tier N50 contig number: 3512

Middle tier (90000000 bp -- 120000000 bp):
  Contig number: 13581
  Average length: 2209 bp
  Longest length: 3326 bp
  Contig bases in this tier: 30001122 bp
 Q20 bases in this tier: 28069618 bp
  Q20 base percentage: 93.5%
  Middle tier N50 contig length: 2313 bp
  Middle tier N50 contig number: 5421

Bottom tier (120000000 bp -- end):
  Contig number: 9573
  Average length: 979 bp
  Longest length: 1418 bp
  Contig bases in this tier: 9369438 bp
  Q20 bases in this tier: 8250716 bp
  Q20 base percentage: 88%
  Bottom tier N50 contig length: 1093 bp
  Bottom tier N50 contig number: 3746



*** Contiguity: Supercontig ***
Total supercontig number: 4670
Average supercontig length: 27703 bp
Maximum supercontig length: 956079 bp
N50 supercontig length: 62153 bp
N50 supercontig number: 558

Major supercontig (> 2000 bp) number: 4454
Major_supercontig bases: 129009969 bp
Major_supercontig Q20 bases: 124256166 bp
Major_supercontig Q20 base percent: 96.3%

Scaffolds > 1M: 0
Scaffold 250K--1M: 24
Scaffold 100K--250K: 230
Scaffold 10--100K: 2547
Scaffold 5--10K: 562
Scaffold 2--5K: 1091
Scaffold 0--2K: 216

Top tier (up to 90000000 bp):
  Supercontig number: 1114
  Average length: 80796 bp
  Longest length: 956079 bp
  Contig bases in this tier: 90006526 bp
  Q20 bases in this tier: 87032180 bp
  Q20 base percentage: 96.6%
  Top tier N50 supercontig length: 93052 bp
  Top tier N50 supercontig number: 296

Middle tier (90000000 bp -- 120000000 bp):
  Supercontig number: 1555
  Average length: 19298 bp
  Longest length: 32727 bp
  Contig bases in this tier: 30008049 bp
  Q20 bases in this tier: 28738176 bp
  Q20 base percentage: 95.7%
  Middle tier N50 supercontig length: 20886 bp
  Middle tier N50 supercontig number: 574

Bottom tier (120000000 bp -- end):
  Supercontig number: 2001
  Average length: 4677 bp
  Longest length: 10921 bp
  Contig bases in this tier: 9358386 bp
  Q20 bases in this tier: 8806416 bp
  Q20 base percentage: 94.1%
  Bottom tier N50 supercontig length: 7431 bp
  Bottom tier N50 supercontig number: 502


*** SNP Stats ***

Unable to find any *snp files to process stats