View source for Marmoset calJac3 13-way size statistics

==see also==

<UL>
<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>
</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 calJac3 matched (chainLink table) == featureBits calJac3 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;calJac3<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://genome.wustl.edu/genomes/view/callithrix_jacchus/ calJac3]</TH>
<TH ALIGN=RIGHT>14,205</TH>
  <TD ALIGN=RIGHT>2,914,958,544</TD><TD ALIGN=RIGHT>2,752,505,800</TD>
  <TD ALIGN=RIGHT>162,452,744</TD><TD ALIGN=RIGHT>%&nbsp;47.71</TD>
  <TD ALIGN=CENTER>Marmoset</TD><TH ALIGN=CENTER>6X</TH>
<TH ALIGN=CENTER>132174527</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>[http://genome.wustl.edu/genomes/view/pongo_abelii/ ponAbe2]</TH>
<TH ALIGN=RIGHT>55</TH>
  <TD ALIGN=RIGHT>3,446,771,396</TD><TD ALIGN=RIGHT>3,093,543,172</TD>
  <TD ALIGN=RIGHT>353,228,224</TD><TD ALIGN=RIGHT>%&nbsp;50.89</TD>
  <TD ALIGN=CENTER>Orangutan</TD><TH ALIGN=CENTER>6X</TH>
<TH ALIGN=CENTER>135191526</TH>
  <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>71.893%</TD>
<TD ALIGN=RIGHT>5000</TD><TD ALIGN=CENTER>medium</TD>
</TR>
<TR><TH ALIGN=RIGHT>03</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>SyntenicNet</TH><TD ALIGN=RIGHT>73.768%</TD>
<TD ALIGN=RIGHT>5000</TD><TD ALIGN=CENTER>medium</TD>
</TR>
<TR><TH ALIGN=RIGHT>04</TH>
<TH ALIGN=RIGHT>[http://genome.wustl.edu/genomes/view/pan_troglodytes/ panTro2]</TH>
<TH ALIGN=RIGHT>52</TH>
  <TD ALIGN=RIGHT>3,350,447,512</TD><TD ALIGN=RIGHT>2,909,246,738</TD>
  <TD ALIGN=RIGHT>441,200,774</TD><TD ALIGN=RIGHT>%&nbsp;48.90</TD>
  <TD ALIGN=CENTER>Chimp</TD><TH ALIGN=CENTER>6X</TH>
<TH ALIGN=CENTER>145085868</TH>
  <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>72.304%</TD>
<TD ALIGN=RIGHT>5000</TD><TD ALIGN=CENTER>medium</TD>
</TR>
<TR><TH ALIGN=RIGHT>05</TH>
<TH ALIGN=RIGHT>[http://www.sanger.ac.uk/resources/downloads/gorillagenomes.html gorGor2]</TH>
<TH ALIGN=RIGHT>58,049</TH>
  <TD ALIGN=RIGHT>3,035,791,622</TD><TD ALIGN=RIGHT>2,829,687,208</TD>
  <TD ALIGN=RIGHT>206,104,414</TD><TD ALIGN=RIGHT>%&nbsp;48.19</TD>
  <TD ALIGN=CENTER>Gorilla</TD><TH ALIGN=CENTER>2X</TH>
<TH ALIGN=CENTER>913458</TH>
  <TD ALIGN=CENTER>RecipBest</TD><TD ALIGN=RIGHT>76.343%</TD>
<TD ALIGN=RIGHT>3000</TD><TD ALIGN=CENTER>medium</TD>
</TR>
<TR><TH ALIGN=RIGHT>06</TH>
<TH ALIGN=RIGHT>[http://www.hgsc.bcm.tmc.edu/project-species-p-Rhesus%20Macaque.hgsc?pageLocation=Rhesus%20Macaque rheMac2]</TH>
<TH ALIGN=RIGHT>22</TH>
  <TD ALIGN=RIGHT>2,864,106,071</TD><TD ALIGN=RIGHT>2,646,668,809</TD>
  <TD ALIGN=RIGHT>217,437,262</TD><TD ALIGN=RIGHT>%&nbsp;48.28</TD>
  <TD ALIGN=CENTER>Rhesus</TD><TH ALIGN=CENTER>5.1X</TH>
<TH ALIGN=CENTER>153947521</TH>
  <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>69.625%</TD>
<TD ALIGN=RIGHT>5000</TD><TD ALIGN=CENTER>medium</TD>
</TR>
<TR><TH ALIGN=RIGHT>07</TH>
<TH ALIGN=RIGHT>[http://www.hgsc.bcm.tmc.edu/project-species-p-Papio%20hamadryas.hgsc?pageLocation=Papio%20hamadryas papHam1]</TH>
<TH ALIGN=RIGHT>387,374</TH>
  <TD ALIGN=RIGHT>2,867,564,654</TD><TD ALIGN=RIGHT>2,741,849,051</TD>
  <TD ALIGN=RIGHT>125,715,603</TD><TD ALIGN=RIGHT>%&nbsp;48.70</TD>
  <TD ALIGN=CENTER>Baboon</TD><TH ALIGN=CENTER>5.3X</TH>
<TH ALIGN=CENTER>88525</TH>
  <TH ALIGN=CENTER>RecipBest</TH><TD ALIGN=RIGHT>70.053%</TD>
<TD ALIGN=RIGHT>5000</TD><TD ALIGN=CENTER>medium</TD>
</TR>
<TR><TH ALIGN=RIGHT>08</TH>
<TH ALIGN=RIGHT>[ftp://ftp.broad.mit.edu/pub/assemblies/mammals/tarsier/Tarsyr1.0/ tarSyr1]</TH>
<TH ALIGN=RIGHT>656,709</TH>
  <TD ALIGN=RIGHT>3,179,905,132</TD><TD ALIGN=RIGHT>2,768,536,343</TD>
  <TD ALIGN=RIGHT>411,368,789</TD><TD ALIGN=RIGHT>%&nbsp;41.75</TD>
  <TD ALIGN=CENTER>Tarsier</TD><TH ALIGN=CENTER>2X</TH>
<TH ALIGN=CENTER>12214</TH>
  <TD ALIGN=CENTER>RecipBest</TD><TD ALIGN=RIGHT>46.729%</TD>
<TD ALIGN=RIGHT>3000</TD><TD ALIGN=CENTER>medium</TD>
</TR>
<TR><TH ALIGN=RIGHT>09</TH>
<TH ALIGN=RIGHT>[http://www.broadinstitute.org/ftp/pub/assemblies/mammals/mouseLemur/MicMur1.0/ micMur1]</TH>
<TH ALIGN=RIGHT>185,042</TH>
  <TD ALIGN=RIGHT>2,902,270,736</TD><TD ALIGN=RIGHT>1,852,394,361</TD>
  <TD ALIGN=RIGHT>1,049,876,375</TD><TD ALIGN=RIGHT>%&nbsp;37.31</TD>
  <TD ALIGN=CENTER>Mouse lemur</TD><TH ALIGN=CENTER>2X</TH>
<TH ALIGN=CENTER>140884</TH>
  <TD ALIGN=CENTER>RecipBest</TD><TD ALIGN=RIGHT>45.726%</TD>
<TD ALIGN=RIGHT>3000</TD><TD ALIGN=CENTER>medium</TD>
</TR>
<TR><TH ALIGN=RIGHT>10</TH>
<TH ALIGN=RIGHT>[http://www.broadinstitute.org/ftp/pub/assemblies/mammals/bushbaby/otoGar1/ otoGar1]</TH>
<TH ALIGN=RIGHT>120,882</TH>
  <TD ALIGN=RIGHT>3,420,058,864</TD><TD ALIGN=RIGHT>1,969,052,059</TD>
  <TD ALIGN=RIGHT>1,451,006,805</TD><TD ALIGN=RIGHT>%&nbsp;34.89</TD>
  <TD ALIGN=CENTER>Bushbaby</TD><TH ALIGN=CENTER>2X</TH>
<TH ALIGN=CENTER>139426</TH>
  <TD ALIGN=CENTER>RecipBest</TD><TD ALIGN=RIGHT>42.743%</TD>
<TD ALIGN=RIGHT>3000</TD><TD ALIGN=CENTER>medium</TD>
</TR>
<TR><TH ALIGN=RIGHT>11</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>SyntenicNet</TH><TD ALIGN=RIGHT>31.310%</TD>
<TD ALIGN=RIGHT>3000</TD><TD ALIGN=CENTER>medium</TD>
</TR>
<TR><TH ALIGN=RIGHT>12</TH>
<TH ALIGN=RIGHT>[http://www.broadinstitute.org/mammals/dog canFam2]</TH>
<TH ALIGN=RIGHT>41</TH>
  <TD ALIGN=RIGHT>2,531,673,953</TD><TD ALIGN=RIGHT>2,384,996,543</TD>
  <TD ALIGN=RIGHT>146,677,410</TD><TD ALIGN=RIGHT>%&nbsp;40.63</TD>
  <TD ALIGN=CENTER>Dog</TD><TH ALIGN=CENTER>7.6X</TH>
<TH ALIGN=CENTER>67211953</TH>
  <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>50.766%</TD>
<TD ALIGN=RIGHT>3000</TD><TD ALIGN=CENTER>medium</TD>
</TR>
<TR><TH ALIGN=RIGHT>13</TH>
<TH ALIGN=RIGHT>[http://www.broadinstitute.org/mammals/opossum monDom5]</TH>
<TH ALIGN=RIGHT>11</TH>
  <TD ALIGN=RIGHT>3,605,631,728</TD><TD ALIGN=RIGHT>3,501,660,299</TD>
  <TD ALIGN=RIGHT>103,971,429</TD><TD ALIGN=RIGHT>%&nbsp;55.95</TD>
  <TD ALIGN=CENTER>Opossum</TD><TH ALIGN=CENTER>6.8X</TH>
<TH ALIGN=CENTER>527952102</TH>
  <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>7.906%</TD>
<TD ALIGN=RIGHT>5000</TD><TD ALIGN=CENTER>loose</TD>
</TR>
</TABLE>