Index of /EvidentialGene/daphnia/daphnia_magna/Genome/altassembly

 Name                                   Last modified       Size  

 Parent Directory                       25-Jan-2016 19:09      -  
 dmag7finall9b-nwbdmag24g7d.gmap.gff.gz 18-Oct-2015 00:39  45.8M  
 dmag7finall9b-nwbdmag24g7d.map.attr    01-Dec-2015 12:23  10.3M  
 nwbdmag24g7d_454AssemblyProject.xml    11-Oct-2015 21:43    18k  
 nwbdmag24g7d_454NewblerMetrics.txt     11-Oct-2015 10:07    44k  
 nwbdmag24g7d_asm.facount               30-Oct-2015 23:31   1.9M  
 nwbdmag24g7d_asm.fasta.gz              17-Oct-2015 23:15  41.9M  
 nwbdmag24g7d_scaf.agp                  05-Jan-2016 14:10   1.5M  
 nwbdmag24g7d_sctg.agp                  05-Jan-2016 14:15   2.5M  

This is an alternate assembly of same genomic DNA, 454 reads, with a newer version of Newbler,
as the public assembly of 2010.  It is marginally improved by 10%, but has not been annotated
nor in public use.  The unassembled reads in this and public set amount to a large fraction of
missing chromosome assembly.

TABLE A6. Assembly details for  nwbdmag24g7d, Newbler v.2.9 (20130529_1641) 
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 Input nReads  = 12785963; nPairs= 3151045; nBases = 3209432352; (TABLE A4)
   Preasm nReads = 15707284; nBases = 2947678588;  after Newbler read processing
 Assembled
   Coverage peakDepth = 13.0; estimatedGenomeSize  = 227.0 MB;
   nAlignedReads    = 10593243  67.44% ;  nAlignedBases    = 2162983966  73.38%; 
   nAssembled       = 10029045  63.85%;   nAssembledBases  =   117483510 (-NNN)
   nProperPaired    =  2016202; nMultiplyMapped = 774430; nOneMapped = 301099
 Unassembled reads (36%):  
   nRepeats = 3332814  21.2%;    nPartial = 562419  3.6%;
   nSingletons = 1736006  11.0%; nOutlier  = 47000  0.3%;
 Scaffolds:   n=2234;  Largest=3111085; N50=564772  
 All contigs: n=72358; bases=119215380    
----------------------------------------------------------------------
  from dapmag454gasm/daphmag24i7c454NewblerMetrics.txt