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 inbredby 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.The Caenorhabditis japonica genome
was sequenced to a depth of 22X. Approximately 6x coverage coming from
plasmid and fosmid reads and approximately 16x 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 Cabog assembler.

*** SIMPLE READ STATS ***
Total input reads: 8545984
Total input bases: 3569550991 bp
Total Q20 bases: 2916243054 bp
Average Q20 bases per read: 341 bp
Average read length: 418 bp
Placed reads: 3677612
  (total reads in scaffold: 4214695)
  (unique reads: 3677612)
  (duplicate reads: 537083)
Unplaced reads: 4868372
Chaff rate: 56.97%
Q20 base redundancy: 18.9X
Total prefin reads input: 0
Total prefin reads unused: 0


*** Contiguity: Contig ***
Total contig number: 35936
Total contig bases: 154066943 bp
Total Q20 bases: 152648139 bp
Q20 bases %: 99%
Average contig length: 4287 bp
Maximum contig length: 151170 bp
N50 contig length: 10164 bp
N50 contig number: 3894

Major contig (> 500 bp) number: 35612
Major_contig bases: 153956199 bp
Major_contig avg contig length: 4323
Major_contig Q20 bases: 152543448 bp
Major_contig Q20 base percent: 99.1%
Major_contig N50 contig length: 10173
Major_contig N50 contig number: 3888

Top tier (up to 62873380 bp): 
  Contig number: 2673
  Average length: 23526 bp
  Longest length: 151170 bp
  Contig bases in this tier: 62886127 bp
  Q20 bases in this tier: 62726784 bp
  Q20 base percentage: 99.7%
  Top tier N50 contig length: 23952 bp
  Top tier N50 contig number: 871

Middle tier (62873380 bp -- 94310070 bp): 
  Contig number: 3288
  Average length: 9562 bp
  Longest length: 13159 bp
  Contig bases in this tier: 31438347 bp
  Q20 bases in this tier: 31295366 bp
  Q20 base percentage: 99.5%
  Middle tier N50 contig length: 9861 bp
  Middle tier N50 contig number: 1377

Bottom tier (94310070 bp -- end): 
  Contig number: 29975
  Average length: 1993 bp
  Longest length: 6811 bp
  Contig bases in this tier: 59742469 bp
  Q20 bases in this tier: 58625989 bp
  Q20 base percentage: 98.1%
  Bottom tier N50 contig length: 2273 bp
  Bottom tier N50 contig number: 7779


*** Contiguity: Supercontig ***
Total supercontig number: 18822
Average supercontig length: 8185 bp
Maximum supercontig length: 1016771 bp
N50 supercontig length: 88104 bp
N50 supercontig number: 426

Major supercontig (> 500 bp) number: 18813
Major_supercontig bases: 154063554 bp
Major_supercontig avg contig length: 8189
Major_supercontig Q20 bases: 152644885 bp
Major_supercontig Q20 base percent: 99.1%
Major_supercontig N50 contig length: 88104
Major_supercontig N50 contig number: 426

Scaffolds > 1M: 1
Scaffold 250K--1M: 72
Scaffold 100K--250K: 284
Scaffold 10--100K: 1536
Scaffold 5--10K: 635
Scaffold 2--5K: 2539
Scaffold 0--2K: 13755

Top tier (up to 62873380 bp): 
  Supercontig number: 285
  Average length: 220703 bp
  Longest length: 1016771 bp
  Contig bases in this tier: 62900238 bp
  Q20 bases in this tier: 62640276 bp
  Q20 base percentage: 99.5%
  Top tier N50 supercontig length: 228214 bp
  Top tier N50 supercontig number: 85

Middle tier (62873380 bp -- 94310070 bp): 
  Supercontig number: 384
  Average length: 81914 bp
  Longest length: 115951 bp
  Contig bases in this tier: 31454889 bp
  Q20 bases in this tier: 31289241 bp
  Q20 base percentage: 99.4%
  Middle tier N50 supercontig length: 86544 bp
  Middle tier N50 supercontig number: 159

Bottom tier (94310070 bp -- end): 
  Supercontig number: 18153
  Average length: 3289 bp
  Longest length: 55846 bp
  Contig bases in this tier: 59711816 bp
  Q20 bases in this tier: 58718622 bp
  Q20 base percentage: 98.3%
  Bottom tier N50 supercontig length: 10559 bp
  Bottom tier N50 supercontig number: 1180


*** Constraints ***
No constraint info for newbler assemblies


*** Genome Contents ***
Total GC count: 60426154, (39.2%)
Total AT count: 93640789, (60.8%)
Total NX count: 0, (0%)
Total: 154066943