View source for Ce10 Genome size statistics

==see also==

<UL>
<LI>June 2011 C. elegans 9-way [[Ce10 conservation alignment]]</LI>
<LI>June 2011 C. elegans 9-way [[Ce10_conservation_lastz_parameters]]<LI>
<LI>all other [[UCSC Multiple Alignments]]</LI>
</UL>

==statistics collected from UCSC 2bit files==
<UL>
<LI>The external link in the first column goes to the FTP location where the genome sequence was obtained</LI>
<LI>The external links from the UCSC database name go to the UCSC genome-test browser for that genome</LI>
<LI>N bases == unknown bases in the assembly marked by &quot;N&quot;</LI>
<LI>non-N bases == called bases in the assembly</LI>
<LI>total size == all bases in assembly, N and non-N</LI>
<LI>The % masked is masking from Repeat Masker or Window Masker plus TRF/Simple Repeats, whichever is greater, usually WindowMasker for these genomes</LI>
<LI>The common name external links go to information pages for this genome</LI>
<LI>The coverage numbers are taken directly from information README files from the sequencing center</LI>
<LI>The N50 size is calculated directly from the UCSC chrom.sizes file which is the size of the chromosomes as seen in the UCSC genome browser</LI>
</UL>

==do not edit, automatically generated table==


<TABLE BORDER=1>
<TR><TH>order<BR>count/<BR>ftp&nbsp;src</TH>
  <TH>ucsc<BR>db&nbsp;name/<BR>genome-preview</TH>
  <TH>chrom<BR>count</TH>
  <TH>total<BR>size</TH>
  <TH>non-N<BR>bases</TH>
  <TH>N&nbsp;base<BR>count</TH>
  <TH>%&nbsp;masked</TH>
  <TH>common&nbsp;name/<BR>src&nbsp;info</TH>
  <TH>coverage</TH>
  <TH>N50<BR>chrom.sizes</TH>
  <TH>alignment&nbsp;type</TH>
  <TH>%&nbsp;of&nbsp;ce10<BR>matched<BR>(chainLink&nbsp;table)</TH>
  <TH>chain<BR>minScore</TH>
  <TH>chain<BR>linearGap</TH>
<TR>
<TR><TH ALIGN=RIGHT>[ftp://ftp.sanger.ac.uk/pub/wormbase/WS220/genomes/c_elegans/ 01]</TH><TH ALIGN=RIGHT>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=ce10 ce10]</TH>
<TH ALIGN=RIGHT>7</TH>
  <TD ALIGN=RIGHT>100,286,070</TD><TD ALIGN=RIGHT>100,286,070</TD>
  <TD ALIGN=RIGHT>0</TD><TD ALIGN=RIGHT>%&nbsp;13.38</TD>
  <TD ALIGN=CENTER>[http://wiki.wormbase.org/index.php/Caenorhabditis_elegans C. elegans]</TD><TH ALIGN=CENTER>30X</TH>
<TH ALIGN=CENTER>17493793</TH>
  <TH ALIGN=CENTER>N/A</TH><TD ALIGN=RIGHT>N/A</TD>
<TD ALIGN=RIGHT>1000</TD>
  <TD ALIGN=CENTER>N/A</TD></TR>
<TR><TH ALIGN=RIGHT>[ftp://ftp.sanger.ac.uk/pub/wormbase/WS225/genomes/c_briggsae/ 02]</TH><TH ALIGN=RIGHT>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=cb4 cb4]</TH>
<TH ALIGN=RIGHT>13</TH>
  <TD ALIGN=RIGHT>108,434,085</TD><TD ALIGN=RIGHT>105,430,959</TD>
  <TD ALIGN=RIGHT>3,003,126</TD><TD ALIGN=RIGHT>%&nbsp;36.52</TD>
  <TD ALIGN=CENTER>[http://www.sanger.ac.uk/Projects/C_briggsae/ C. briggsae]</TD><TH ALIGN=CENTER>10X</TH>
<TH ALIGN=CENTER>17485439</TH>
  <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>39.386%</TD>
<TD ALIGN=RIGHT>1000</TD>
  <TD ALIGN=CENTER>loose</TD></TR>
<TR><TH ALIGN=RIGHT>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_sp_9_MAF_2010/Caenorhabditis_sp9_JU1422-3.0.1/ 03]</TH><TH ALIGN=RIGHT>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=caeSp91 caeSp91]</TH>
<TH ALIGN=RIGHT>7,636</TH>
  <TD ALIGN=RIGHT>204,396,809</TD><TD ALIGN=RIGHT>186,540,270</TD>
  <TD ALIGN=RIGHT>17,856,539</TD><TD ALIGN=RIGHT>%&nbsp;31.67</TD>
  <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AENM01 C. sp. 9 ju1422]</TD><TH ALIGN=CENTER>37.6X</TH>
<TH ALIGN=CENTER>196652</TH>
  <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>42.169%</TD>
<TD ALIGN=RIGHT>1000</TD>
  <TD ALIGN=CENTER>loose</TD></TR>
<TR><TH ALIGN=RIGHT>[ftp://ftp.sanger.ac.uk/pub/wormbase/WS220/genomes/c_remanei/ 04]</TH><TH ALIGN=RIGHT>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=caeRem4 caeRem4]</TH>
<TH ALIGN=RIGHT>3,670</TH>
  <TD ALIGN=RIGHT>145,442,736</TD><TD ALIGN=RIGHT>138,406,203</TD>
  <TD ALIGN=RIGHT>7,036,533</TD><TD ALIGN=RIGHT>%&nbsp;30.48</TD>
  <TD ALIGN=CENTER>[http://genome.wustl.edu/genomes/view/caenorhabditis_remanei/ C. remanei]</TD><TH ALIGN=CENTER>9.2X</TH>
<TH ALIGN=CENTER>435512</TH>
  <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>41.722%</TD>
<TD ALIGN=RIGHT>1000</TD>
  <TD ALIGN=CENTER>loose</TD></TR>
<TR><TH ALIGN=RIGHT>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_sp_9_MAF_2010/Caenorhabditis_sp9_JU1422-3.0.1/ 05]</TH><TH ALIGN=RIGHT>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=caeSp111 caeSp111]</TH>
<TH ALIGN=RIGHT>665</TH>
  <TD ALIGN=RIGHT>79,321,433</TD><TD ALIGN=RIGHT>76,497,192</TD>
  <TD ALIGN=RIGHT>2,824,241</TD><TD ALIGN=RIGHT>%&nbsp;29.15</TD>
  <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AEKS01 C. sp. 11 ju1373]</TD><TH ALIGN=CENTER>20.2X</TH>
<TH ALIGN=CENTER>20921866</TH>
  <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>37.876%</TD>
<TD ALIGN=RIGHT>1000</TD>
  <TD ALIGN=CENTER>loose</TD></TR>
<TR><TH ALIGN=RIGHT>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_brenneri/C_brenneri-6.0.1b/ 06]</TH><TH ALIGN=RIGHT>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=caePb3 caePb3]</TH>
<TH ALIGN=RIGHT>3,307</TH>
  <TD ALIGN=RIGHT>190,374,847</TD><TD ALIGN=RIGHT>170,097,428</TD>
  <TD ALIGN=RIGHT>20,277,419</TD><TD ALIGN=RIGHT>%&nbsp;29.30</TD>
  <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ABEG02 C. brenneri]</TD><TH ALIGN=CENTER>9.5X</TH>
<TH ALIGN=CENTER>381961</TH>
  <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>40.644%</TD>
<TD ALIGN=RIGHT>1000</TD>
  <TD ALIGN=CENTER>loose</TD></TR>
<TR><TH ALIGN=RIGHT>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_sp_7_MAF_2007/Caenorhabditis_sp7_JU1286-4.0.1/ 07]</TH><TH ALIGN=RIGHT>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=caeSp71 caeSp71]</TH>
<TH ALIGN=RIGHT>52,546</TH>
  <TD ALIGN=RIGHT>196,410,749</TD><TD ALIGN=RIGHT>177,605,791</TD>
  <TD ALIGN=RIGHT>18,804,958</TD><TD ALIGN=RIGHT>%&nbsp;31.53</TD>
  <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AENL01 C. sp. 7 ju1286]</TD><TH ALIGN=CENTER>37.9X</TH>
<TH ALIGN=CENTER>73785</TH>
  <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>40.236%</TD>
<TD ALIGN=RIGHT>1000</TD>
  <TD ALIGN=CENTER>loose</TD></TR>
<TR><TH ALIGN=RIGHT>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_japonica/C_japonica-7.0.1/ 08]</TH><TH ALIGN=RIGHT>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=caeJap4 caeJap4]</TH>
<TH ALIGN=RIGHT>18,817</TH>
  <TD ALIGN=RIGHT>166,256,191</TD><TD ALIGN=RIGHT>154,057,934</TD>
  <TD ALIGN=RIGHT>12,198,257</TD><TD ALIGN=RIGHT>%&nbsp;46.77</TD>
  <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ABLE03 C. japonica]</TD><TH ALIGN=CENTER>22X</TH>
<TH ALIGN=CENTER>94149</TH>
  <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>27.737%</TD>
<TD ALIGN=RIGHT>1000</TD>
  <TD ALIGN=CENTER>loose</TD></TR>
<TR><TH ALIGN=RIGHT>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_sp_PS1010/ps1010rel4/ 09]</TH><TH ALIGN=RIGHT>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=caeAng1 caeAng1]</TH>
<TH ALIGN=RIGHT>33,559</TH>
  <TD ALIGN=RIGHT>79,761,545</TD><TD ALIGN=RIGHT>75,258,781</TD>
  <TD ALIGN=RIGHT>4,502,764</TD><TD ALIGN=RIGHT>%&nbsp;38.31</TD>
  <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AEHI01 C. angaria]</TD><TH ALIGN=CENTER>170X</TH>
<TH ALIGN=CENTER>9453</TH>
  <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>17.625%</TD>
<TD ALIGN=RIGHT>1000</TD>
  <TD ALIGN=CENTER>loose</TD></TR>
</TABLE>