View source for DanRer10 12-way Genome size statistics

==see also==

<UL>
<LI>Zebrafish 12-way [[DanRer10 12-way conservation alignment]]</LI>
<LI>Zebrafish 12-way [[DanRer10 12-way 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-preview 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;danRer10<BR>matched<BR>(chainLink&nbsp;table)</TH>
  <TH>chain<BR>minScore</TH>
  <TH>chain<BR>linearGap</TH>
<TR>
<TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/assembly/GCF_000002035.5 01]</TH><TH ALIGN=RIGHT>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=danRer10 danRer10]</TH>
<TH ALIGN=RIGHT>1,061</TH>
  <TD ALIGN=RIGHT>1,371,719,383</TD><TD ALIGN=RIGHT>1,369,631,918</TD>
  <TD ALIGN=RIGHT>2,087,465</TD><TD ALIGN=RIGHT>%&nbsp;52.32</TD>
  <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=CABZ01 Zebrafish]</TD><TH ALIGN=CENTER>30X</TH>
<TH ALIGN=CENTER>53345113</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>[ftp://ftp.broadinstitute.org/pub/assemblies/fish/stickleback/gasAcu1/ 02]</TH><TH ALIGN=RIGHT>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=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>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AANH01 Stickleback]</TD><TH ALIGN=CENTER>6X</TH>
<TH ALIGN=CENTER>20083130</TH>
  <TH ALIGN=CENTER>Net</TH><TD ALIGN=RIGHT>9.814%</TD>
<TD ALIGN=RIGHT>2000</TD>
  <TD ALIGN=CENTER>medium</TD></TR>
<TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/assembly/GCA_000242695.1/ 03]</TH><TH ALIGN=RIGHT>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=lepOcu1 lepOcu1]</TH>
<TH ALIGN=RIGHT>1,925</TH>
  <TD ALIGN=RIGHT>945,874,548</TD><TD ALIGN=RIGHT>869,414,359</TD>
  <TD ALIGN=RIGHT>76,460,189</TD><TD ALIGN=RIGHT>%&nbsp;24.85</TD>
  <TD ALIGN=CENTER>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_other/Lepisosteus_oculatus/LepOcu1/ Spotted gar]</TD><TH ALIGN=CENTER>677.5X</TH>
<TH ALIGN=CENTER>50348508</TH>
  <TH ALIGN=CENTER>Net</TH><TD ALIGN=RIGHT>8.409%</TD>
<TD ALIGN=RIGHT>5000</TD>
  <TD ALIGN=CENTER>loose</TD></TR>
<TR><TH ALIGN=RIGHT>[http://www.genoscope.cns.fr/spip/Tetraodon-nigroviridis-a-fish-with.html 04]</TH><TH ALIGN=RIGHT>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=tetNig2 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>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=CAAE01 Tetraodon]</TD><TH ALIGN=CENTER>7.9X</TH>
<TH ALIGN=CENTER>13390619</TH>
  <TH ALIGN=CENTER>Net</TH><TD ALIGN=RIGHT>6.063%</TD>
<TD ALIGN=RIGHT>2000</TD>
  <TD ALIGN=CENTER>medium</TD></TR>
<TR><TH ALIGN=RIGHT>[http://www.fugu-sg.org/ 05]</TH><TH ALIGN=RIGHT>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=fr3 fr3]</TH>
<TH ALIGN=RIGHT>6,835</TH>
  <TD ALIGN=RIGHT>391,484,715</TD><TD ALIGN=RIGHT>350,961,831</TD>
  <TD ALIGN=RIGHT>40,522,884</TD><TD ALIGN=RIGHT>%&nbsp;19.01</TD>
  <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=CAAB02 Fugu]</TD><TH ALIGN=CENTER>8.5X</TH>
<TH ALIGN=CENTER>11516971</TH>
  <TH ALIGN=CENTER>Net</TH><TD ALIGN=RIGHT>7.080%</TD>
<TD ALIGN=RIGHT>2000</TD>
  <TD ALIGN=CENTER>medium</TD></TR>
<TR><TH ALIGN=RIGHT>[http://dolphin.lab.nig.ac.jp/medaka/index.php 06]</TH><TH ALIGN=RIGHT>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=oryLat2 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>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=BAAE01 Medaka]</TD><TH ALIGN=CENTER>10.6X</TH>
<TH ALIGN=CENTER>29908082</TH>
  <TH ALIGN=CENTER>Net</TH><TD ALIGN=RIGHT>9.640%</TD>
<TD ALIGN=RIGHT>2000</TD>
  <TD ALIGN=CENTER>medium</TD></TR>
<TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/assembly/GCF_000004195.3/ 07]</TH><TH ALIGN=RIGHT>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=xenTro9 xenTro9]</TH>
<TH ALIGN=RIGHT>6,822</TH>
  <TD ALIGN=RIGHT>1,440,398,454</TD><TD ALIGN=RIGHT>1,369,865,365</TD>
  <TD ALIGN=RIGHT>70,533,089</TD><TD ALIGN=RIGHT>%&nbsp;34.42</TD>
  <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AAMC03 X. tropicalis]</TD><TH ALIGN=CENTER>7.6X</TH>
<TH ALIGN=CENTER>135134832</TH>
  <TH ALIGN=CENTER>Net</TH><TD ALIGN=RIGHT>6.731%</TD>
<TD ALIGN=RIGHT>5000</TD>
  <TD ALIGN=CENTER>loose</TD></TR>
<TR><TH ALIGN=RIGHT>[ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/315/GCF_000002315.5_GRCg6a/ 08]</TH><TH ALIGN=RIGHT>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=galGal6 galGal6]</TH>
<TH ALIGN=RIGHT>464</TH>
  <TD ALIGN=RIGHT>1,065,365,425</TD><TD ALIGN=RIGHT>1,055,580,959</TD>
  <TD ALIGN=RIGHT>9,784,466</TD><TD ALIGN=RIGHT>%&nbsp;21.41</TD>
  <TD ALIGN=CENTER>[https://www.ncbi.nlm.nih.gov/assembly/GCF_000002315.5/ Chicken]</TD><TH ALIGN=CENTER>82X</TH>
<TH ALIGN=CENTER>91315245</TH>
  <TH ALIGN=CENTER>Net</TH><TD ALIGN=RIGHT>5.871%</TD>
<TD ALIGN=RIGHT>1000</TD>
  <TD ALIGN=CENTER>loose</TD></TR>
<TR><TH ALIGN=RIGHT>[https://www.ncbi.nlm.nih.gov/assembly/GCF_000165045.1/ 09]</TH><TH ALIGN=RIGHT>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=calMil1 calMil1]</TH>
<TH ALIGN=RIGHT>21,204</TH>
  <TD ALIGN=RIGHT>974,498,586</TD><TD ALIGN=RIGHT>936,953,443</TD>
  <TD ALIGN=RIGHT>37,545,143</TD><TD ALIGN=RIGHT>%&nbsp;28.08</TD>
  <TD ALIGN=CENTER>[https://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AAVX02 Elephant shark]</TD><TH ALIGN=CENTER>19.25X</TH>
<TH ALIGN=CENTER>4521921</TH>
  <TH ALIGN=CENTER>Net</TH><TD ALIGN=RIGHT>5.599%</TD>
<TD ALIGN=RIGHT>5000</TD>
  <TD ALIGN=CENTER>loose</TD></TR>
<TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/assembly/GCA_000001405.15/ 10]</TH><TH ALIGN=RIGHT>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=hg38 hg38]</TH>
<TH ALIGN=RIGHT>640</TH>
  <TD ALIGN=RIGHT>3,272,116,950</TD><TD ALIGN=RIGHT>3,110,748,256</TD>
  <TD ALIGN=RIGHT>161,368,694</TD><TD ALIGN=RIGHT>%&nbsp;52.11</TD>
  <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/index.shtml Human]</TD><TH ALIGN=CENTER>20X</TH>
<TH ALIGN=CENTER>145138636</TH>
  <TH ALIGN=CENTER>Net</TH><TD ALIGN=RIGHT>7.110%</TD>
<TD ALIGN=RIGHT>5000</TD>
  <TD ALIGN=CENTER>loose</TD></TR>
<TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/genome/assembly/327618/ 11]</TH><TH ALIGN=RIGHT>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=mm10 mm10]</TH>
<TH ALIGN=RIGHT>66</TH>
  <TD ALIGN=RIGHT>2,730,871,774</TD><TD ALIGN=RIGHT>2,652,783,500</TD>
  <TD ALIGN=RIGHT>78,088,274</TD><TD ALIGN=RIGHT>%&nbsp;45.18</TD>
  <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/bioproject/51977 Mouse]</TD><TH ALIGN=CENTER>20X</TH>
<TH ALIGN=CENTER>130694993</TH>
  <TH ALIGN=CENTER>Net</TH><TD ALIGN=RIGHT>5.228%</TD>
<TD ALIGN=RIGHT>5000</TD>
  <TD ALIGN=CENTER>loose</TD></TR>
<TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/bioproject/56111 12]</TH><TH ALIGN=RIGHT>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=latCha1 latCha1]</TH>
<TH ALIGN=RIGHT>22,819</TH>
  <TD ALIGN=RIGHT>2,860,591,921</TD><TD ALIGN=RIGHT>2,183,592,768</TD>
  <TD ALIGN=RIGHT>676,999,153</TD><TD ALIGN=RIGHT>%&nbsp;45.68</TD>
  <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AFYH00 Coelacanth]</TD><TH ALIGN=CENTER>77.5X</TH>
<TH ALIGN=CENTER>924513</TH>
  <TH ALIGN=CENTER>Net</TH><TD ALIGN=RIGHT>6.319%</TD>
<TD ALIGN=RIGHT>5000</TD>
  <TD ALIGN=CENTER>loose</TD></TR>
</TABLE>