View source for DanRer7 Genome size statistics

==see also==

<UL>
<LI>[[DanRer7 conservation alignment]]</LI>
<LI>[[DanRer7 conservation lastz parameters]]</LI>
<LI>[[Hg19 conservation alignment]]</LI>
<LI>[[Hg19 conservation lastz parameters]]</LI>
<LI>[[Hg18 44way alignment]]</LI>
<LI>[[Hg18 44way blastz parameters]]</LI>
<LI>[[Genome size statistics|Hg18 genome size statistics]]</LI>
<LI>[[Marmoset calJac3 13-way size statistics]]</LI>
</UL>

==statistics collected from UCSC 2bit files==
<UL>
<LI>The external links from the UCSC database name go to the sequencing center information pages for this genome</LI>
<LI>N bases == unknown bases in the assembly marked by 'N'</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 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>
<LI>% masked == masked either with WindowMasker or RepeatMasker plus TRF simple repeats</LI>
<LI>% of danRer7 matched (chainLink table) == featureBits danRer7 chain<Db>Link == alignment coverage</LI>
</UL>

==do not edit, automatically generated table==
<TABLE BORDER=1>
<TR><TH>order<BR>count</TH>
  <TH>ucsc<BR>db&nbsp;name</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</TH>
  <TH>coverage</TH>
  <TH>N50<BR>chrom.sizes</TH>
  <TH>alignment&nbsp;type</TH>
  <TH>%&nbsp;of&nbsp;danRer7<BR>matched<BR>(chainLink&nbsp;table)</TH>
  <TH>chain<BR>minScore</TH>
  <TH>chain<BR>linearGap</TH>
<TR>
<TR><TH ALIGN=RIGHT>01</TH><TH ALIGN=RIGHT>[http://www.sanger.ac.uk/Projects/D_rerio/Zv9_assembly_information.shtml danRer7]</TH>
<TH ALIGN=RIGHT>1,133</TH>
  <TD ALIGN=RIGHT>1,412,464,843</TD><TD ALIGN=RIGHT>1,409,770,109</TD>
  <TD ALIGN=RIGHT>2,694,734</TD><TD ALIGN=RIGHT>%&nbsp;52.06</TD>
  <TD ALIGN=CENTER>Zebrafish</TD><TH ALIGN=CENTER>30X</TH>
<TH ALIGN=CENTER>54093808</TH>
  <TH ALIGN=CENTER>N/A</TH><TD ALIGN=RIGHT>N/A</TD>
<TD ALIGN=RIGHT>N/A</TD>
  <TD ALIGN=CENTER>N/A</TD></TR>
<TR><TH ALIGN=RIGHT>02</TH><TH ALIGN=RIGHT>[ftp://ftp.broad.mit.edu/pub/assemblies/fish/stickleback/gasAcu1/ gasAcu1]</TH>
<TH ALIGN=RIGHT>23</TH>
  <TD ALIGN=RIGHT>463,354,448</TD><TD ALIGN=RIGHT>446,627,861</TD>
  <TD ALIGN=RIGHT>16,726,587</TD><TD ALIGN=RIGHT>%&nbsp;2.58</TD>
  <TD ALIGN=CENTER>Stickleback</TD><TH ALIGN=CENTER>6X</TH>
<TH ALIGN=CENTER>20083130</TH>
  <TH ALIGN=CENTER>MAF net</TH><TD ALIGN=RIGHT>10.270%</TD>
<TD ALIGN=RIGHT>2000</TD>
  <TD ALIGN=CENTER>medium</TD></TR>
<TR><TH ALIGN=RIGHT>03</TH><TH ALIGN=RIGHT>[http://dolphin.lab.nig.ac.jp/medaka/index.php oryLat2]</TH>
<TH ALIGN=RIGHT>7,189</TH>
  <TD ALIGN=RIGHT>869,000,216</TD><TD ALIGN=RIGHT>700,386,597</TD>
  <TD ALIGN=RIGHT>168,613,619</TD><TD ALIGN=RIGHT>%&nbsp;33.09</TD>
  <TD ALIGN=CENTER>Medaka</TD><TH ALIGN=CENTER>10.6X</TH>
<TH ALIGN=CENTER>29908082</TH>
  <TH ALIGN=CENTER>MAF net</TH><TD ALIGN=RIGHT>10.032%</TD>
<TD ALIGN=RIGHT>2000</TD>
  <TD ALIGN=CENTER>medium</TD></TR>
<TR><TH ALIGN=RIGHT>04</TH><TH ALIGN=RIGHT>[http://www.genoscope.cns.fr/spip/Tetraodon-nigroviridis-a-fish-with.html tetNig2]</TH>
<TH ALIGN=RIGHT>27</TH>
  <TD ALIGN=RIGHT>358,618,246</TD><TD ALIGN=RIGHT>302,314,788</TD>
  <TD ALIGN=RIGHT>56,303,458</TD><TD ALIGN=RIGHT>%&nbsp;20.27</TD>
  <TD ALIGN=CENTER>Tetraodon</TD><TH ALIGN=CENTER>7.9X</TH>
<TH ALIGN=CENTER>13390619</TH>
  <TH ALIGN=CENTER>MAF net</TH><TD ALIGN=RIGHT>6.273%</TD>
<TD ALIGN=RIGHT>2000</TD>
  <TD ALIGN=CENTER>medium</TD></TR>
<TR><TH ALIGN=RIGHT>05</TH><TH ALIGN=RIGHT>[http://genome.jgi-psf.org/Takru4/Takru4.info.html fr2]</TH>
<TH ALIGN=RIGHT>2</TH>
  <TD ALIGN=RIGHT>400,525,790</TD><TD ALIGN=RIGHT>351,212,245</TD>
  <TD ALIGN=RIGHT>49,313,545</TD><TD ALIGN=RIGHT>%&nbsp;19.01</TD>
  <TD ALIGN=CENTER>Fugu</TD><TH ALIGN=CENTER>8.5X</TH>
<TH ALIGN=CENTER>400509343</TH>
  <TH ALIGN=CENTER>MAF net</TH><TD ALIGN=RIGHT>7.363%</TD>
<TD ALIGN=RIGHT>2000</TD>
  <TD ALIGN=CENTER>medium</TD></TR>
<TR><TH ALIGN=RIGHT>06</TH><TH ALIGN=RIGHT>[http://genome.jgi-psf.org/Xentr4/Xentr4.info.html xenTro2]</TH>
<TH ALIGN=RIGHT>19,759</TH>
  <TD ALIGN=RIGHT>1,513,925,492</TD><TD ALIGN=RIGHT>1,359,400,017</TD>
  <TD ALIGN=RIGHT>154,525,475</TD><TD ALIGN=RIGHT>%&nbsp;19.65</TD>
  <TD ALIGN=CENTER>X. tropicalis</TD><TH ALIGN=CENTER>7.65X</TH>
<TH ALIGN=CENTER>1564123</TH>
  <TH ALIGN=CENTER>MAF net</TH><TD ALIGN=RIGHT>6.428%</TD>
<TD ALIGN=RIGHT>5000</TD>
  <TD ALIGN=CENTER>loose</TD></TR>
<TR><TH ALIGN=RIGHT>07</TH><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/mouse/index.shtml mm9]</TH>
<TH ALIGN=RIGHT>35</TH>
  <TD ALIGN=RIGHT>2,725,765,481</TD><TD ALIGN=RIGHT>2,620,345,972</TD>
  <TD ALIGN=RIGHT>105,419,509</TD><TD ALIGN=RIGHT>%&nbsp;44.09</TD>
  <TD ALIGN=CENTER>Mouse</TD><TH ALIGN=CENTER>20X</TH>
<TH ALIGN=CENTER>131738871</TH>
  <TH ALIGN=CENTER>MAF net</TH><TD ALIGN=RIGHT>5.104%</TD>
<TD ALIGN=RIGHT>5000</TD>
  <TD ALIGN=CENTER>loose</TD></TR>
<TR><TH ALIGN=RIGHT>08</TH><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/data/index.shtml hg19]</TH>
<TH ALIGN=RIGHT>93</TH>
  <TD ALIGN=RIGHT>3,137,161,264</TD><TD ALIGN=RIGHT>2,897,310,462</TD>
  <TD ALIGN=RIGHT>239,850,802</TD><TD ALIGN=RIGHT>%&nbsp;50.63</TD>
  <TD ALIGN=CENTER>Human</TD><TH ALIGN=CENTER>20X</TH>
<TH ALIGN=CENTER>146364022</TH>
  <TH ALIGN=CENTER>MAF net</TH><TD ALIGN=RIGHT>6.151%</TD>
<TD ALIGN=RIGHT>5000</TD>
  <TD ALIGN=CENTER>loose</TD></TR>
</TABLE>