Index of /genome/Daphnia_magna/openaccess/genes/Genome/genbank_submit

      Name                             Last modified       Size  Description

[DIR] Parent Directory 25-Jan-2016 19:09 - [   ] daphmagna_2011pubfc8.aa.gz 16-Jan-2016 16:15 5.1M [   ] daphmagna_2011pubfc8.gbf.gz 16-Jan-2016 16:28 65.0M [   ] daphmagna_2011pubfc8.gff3.gz 16-Jan-2016 16:15 14.4M [TXT] daphmagna_2011pubfc8.idtab 25-Jan-2016 19:38 2.1M [   ] daphmagna_2011pubfc8.tbl.gz 16-Jan-2016 16:16 3.3M [TXT] daphmagna_2011pubfc8.valsum 16-Jan-2016 16:29 1k [TXT] dmagna20100422asmfixed.agp 16-Jan-2016 14:11 2.1M [TXT] dmagna20100422asmfixed.fa.count 25-Jan-2016 19:22 1012k [   ] dmagna20100422asmfixed.fa.gz 16-Jan-2016 14:13 38.0M [TXT] dmagna20100422asmfixed.fachanges 13-Jan-2016 21:02 1k [   ] dmagna20100422asmfixed.qual.gz 16-Jan-2016 14:35 14.5M [TXT] dmagna20100422asminfo.txt 25-Jan-2016 19:46 9k

Tables on Daphnia magna chromosome assemblies of 454 gdna
Don Gilbert, 2016 Jan 

from:   genomes@ncbi.nlm.nih.gov
to:     gilbertd@indiana.edu
date:   Thu, Jan 21, 2016 at 8:46 AM
subject:        Accession Daphnia magna Xinb3 (LRGB00000000 ; BioSample SAMN03703141)

We have assigned the following accession number to your submission:

SUBID           BioProject      BioSample       Accession       Organism
---------------------------------------------------
SUB1303216      PRJNA298946     SAMN03703141    LRGB00000000    Daphnia magna Xinb3

This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank
under the accession LRGB00000000. The version described in this paper
is version LRGB01000000.

Submission file set
------------------------------------------------------------------------
   5.1M Jan 16 16:15 daphmagna_2011pubfc8.aa.gz	    : proteins of genes
    14M Jan 16 16:15 daphmagna_2011pubfc8.gff3.gz   : gene annotation in GFF format, from daphmagna_201104m8
   2.1M Jan 25 19:38 daphmagna_2011pubfc8.idtab     : table of gene ids, public, original, and evg7 hybrid 
                                                      Dapma1EVg0000000t1, m8AUGnnnn, Dapma7bEVm000000t1
   3.3M Jan 16 16:16 daphmagna_2011pubfc8.tbl.gz    : annotation tbl format (genbank tbl2asn)
    65M Jan 16 16:28 daphmagna_2011pubfc8.gbf.gz    : annotation genbank format
    269 Jan 16 16:29 daphmagna_2011pubfc8.valsum    : tbl2asn val error summary

   2.1M Jan 16 14:11 dmagna20100422asmfixed.agp     : contig to scaffold AGP table
    38M Jan 16 14:13 dmagna20100422asmfixed.fa.gz   : chromosome assembly sequence
  1012K Jan 25 19:22 dmagna20100422asmfixed.fa.count: chr asm scaffold/contig size table (faCount)
    15M Jan 16 14:35 dmagna20100422asmfixed.qual.gz : chr assembly quality scores
    868 Jan 13 21:02 dmagna20100422asmfixed.fachanges : changed scaffolds (excluding drops)

Supporting tables 
------------------------------------------------------------------------

TABLE A1. Chromosome assemblies of Daphnia magna, 12? chromosomes, of size 
          estimated at 220 megabases (flow cyto. [ref]), and 227 mb (newbler)
----------------------------------------------------------------------
Chr.assembly  Megabases  N50  N50s  Big    AsmMethod     DataSource
----------------------------------------------------------------------
a. dmag10         108    64   293k  3.1m  Newbler,2010    3209mb/15m 454 reads
b. dmag24nwb7d    118    68   304k  2.8m  Newbler,2013    3209mb/15m 454 reads (same as a.)
   .. others ..
----------------------------------------------------------------------
  Megabases: total chr. assembly size, minus gaps;  Big: size of largest chr piece; 
  N50: count of chr scaffold pieces at 50% base total; N50s: size of scaffold piece at N50; 
  Daphnia magna chromosome assemblies
  dmag10asm     : 2010, v2.4, 454 gdna reads, 2010 Newbler version
  nwbdmag24g7d  : 2015, 454 data of 2010, 2013 Newbler version, -scaffold option
----------------------------------------------------------------------

TABLE A5.  Assembly details for  dmag10, Newbler v.2.3  (091027_1459)
----------------------------------------------------------------------
 Input nReads  = 12785963; nPairs= 3151045; nBases = 3209432352; (TABLE A4)
   Preasm nReads = 15058514; nBases = 2822113419;   after Newbler read processing
 Assembled
   coverage peakDepth = 13.0; estimatedGenomeSize  = 217.0 MB;
   nAlignedReads    = 8552579  56.8% ;  nAlignedBases    = 1819200804  64.5%; 
   nAssembled       = 8244025  54.7%;   nAssembledBases  =  107787551 (-NNN)
   nProperPaired    = 1423127; nMultiplyMapped = 1048421; nOneMapped = 350651
 Unassembled reads (46%):  
   nRepeats  = 5595508  37.2%;  nPartial = 304740  2.2%;
   nSingletons = 862293  5.7%;  nOutlier  = 51948  0.4%;
 Scaffolds:   n=3405;  Largest=3718170; N50=545719
 All contigs: n=50114; bases=107787551    
----------------------------------------------------------------------
  from  dapmag454gasm/daphmag10geno454NewblerMetrics.txt

TABLE A4. Daphnia magna 454 gDNA read sets, BioProject PRJNA298946, Study SRP064876
---------------------------------------------------------------------------------
Runtype   nPair  megaBases  nReads  SRA Accessions and File names
-------   -----  ---------  ------  -------------------------------------------------
  EXPERIMENT  reads08               SRX1340073,SRR2664925
SINGLE    0       110.5M    546371  reads.s01r1,reads.s01r2,
SINGLE    0       96.5M     466922  reads.s02r1,reads.s02r2,
SINGLE    0       114.0M    541922  reads.s03r1,reads.s03r2,
SINGLE    0       104.4M    482531  reads.s04r2,reads.s04r1,
SINGLE    0       100.8M    500205  reads.s05r1,reads.s05r2,
SINGLE    0       96.3M     471434  reads.s06r1,reads.s06r2,
  EXPERIMENT  reads10               SRX1341854,SRR2671171
SINGLE    0       303.8M    1065082 reads.s15r2,reads.s15r1,
SINGLE    0       317.3M    1072889 reads.s16l1r1,reads.s16l1r2,
SINGLE    0       141.6M    590937  reads.s16l3r1,reads.s16l3r2,reads.s16l3r4,
  EXPERIMENT  pairs08i3k            SRX1341948,SRR2671679    insert 2.3kb
PAIRED    209463  127.2M    518690  pairs.s7r2,pairs.s7r1,
PAIRED    168944  108.1M    477436  pairs.s8r1,pairs.s8r2,
PAIRED    195512  118.3M    485444  pairs.s9r1,pairs.s9r2,
PAIRED    200726  122.3M    506555  pairs.s10r2,pairs.s10r1,
PAIRED    222427  133.4M    535542  pairs.s11r2,pairs.s11r1,
PAIRED    217507  131.8M    533032  pairs.s12r2,pairs.s12r1,
PAIRED    245720  149.3M    602317  pairs.s13r1,pairs.s13r2,
  EXPERIMENT  pairs09i20k           SRX1342036,SRR2671858   insert 20kb 
PAIRED    268617  158.0M    532372  pairs.s14l1r2,pairs.s14l1r3,pairs.s14l1r1,pairs.s14l1r4,
PAIRED    289298  174.6M    592954  pairs.s14l2r6,pairs.s14l2r5,pairs.s14l2r7,pairs.s14l2r8,
PAIRED    244300  144.4M    548692  pairs.s14l3r1,pairs.s14l3r2,pairs.s14l3r3,pairs.s14l3r4,
PAIRED    255748  135.1M    568084  pairs.s14l4r5,pairs.s14l4r6,pairs.s14l4r7,pairs.s14l4r8,
  EXPERIMENT  pairs10i8k            SRX1341868,SRR2671211   insert 8kb
PAIRED    632783  321.5M    1146552 pairs.s15r1,pairs.s15r2
------  -------- ---------  -------------------------------------------------------
Total  3,151,045 3,209M  12,785,963 
---------------------------------------------------------------------------------


TABLE A9. Daphnia magna annotated genome submission notes, BioProject PRJNA298946.
---------------------------------------------------------------------------------

version daphmagna_2011pubfc7 (fc7b) ann/asm submitted to ncbi genomes, 2016.01.14
tbl2asn warnings in annotation
     2 WARNING: SEQ_FEAT.MultipleGeneOverlap    : checked, not cds-overlap but intronic genes
   141 WARNING: SEQ_FEAT.ShortExon              : checked, mostly high value genes 
   370 WARNING: SEQ_GRAPH.GraphNScore           : qual score>0 but low, Newbler calls N for low-qual bases
    10 WARNING: SEQ_FEAT.NotSpliceConsensusAcceptor :
    10 WARNING: SEQ_FEAT.NotSpliceConsensusDonor    :
   462 INFO:    SEQ_FEAT.RareSpliceConsensusDonor

ShortExon genes (n=141):
  These have been checked and are mostly high value genes (123 orthologs,
  133 with expressed transcript equivalents) where tiny exons (some 2,3
  bases) were generated by a gene modeller. Though probable artifact
  exons, the gene proteins are checked, valid and valuable (published on).

Changes to original chromosome assembly of 2010:
  dmagna-v2.4-20100422-assembly contains 40357 entries (3405 scaffolds, 36951 contigs)
  - 28956 are submitted as chromosome parts (3404 scaffolds, 25552 contigs)
  - 28 entries removed as possible vector or rRNA contaminants (1 scaffold, 27 contigs)
  - 11372 tiny contigs removed (size < 200 nt), a few had low qual fragment gene models
  - 20 entries were trimmed of NN or vectors (6 scaffolds, 14 contigs), by up to 38 bases.
  
Changes to original gene set of 2011:
  daphmagna_2011 public gene set includes 34614 loci (many annotated as non-coding)
    -- 26701 submitted as gene loci, no alternate transcripts
       NCBI locus_tag APZ42_000000 corresponding to wfleabase.org GeneID Dapma1EVg000000
    -- 14 genes are included as gene fragment misc_feature, due to discrepancies w/ ncbi model
    -- 7905 are removed for various reasons: 
      2481 tiny/fragment, 2950 lowval, 1432 transposon genes, 
      572 partial-warns, 339 on tiny-scaffolds, 102 overlap-genes,
      15 innerstop, 8 contaminant, 4 scaffold-removed
  annotations include original id notes "original-id m8AUGepir2s00001g2t1"
  annotations include improved hybrid 2014 gene set equivalence "genes-ver7-id Dapma7bEVm030035t1"

Changes v2 (ncbi-fcs):
  -- removed 155 tiny contigs flags as contaminant (size 988..202, mostly Thermus thermophilus bacteria)
  -- contig fcs-removal took out 55 gene models, all 1-exon, likely fragment, bacterial genes
  
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