View source for Hg38 5-way Genome size statistics

==see also==

<UL>
<LI>Human 5-way [[Hg38 5-way conservation alignment]]</LI>
<LI>Human 5-way [[Hg38 5-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;hg38<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/GCA_000001405.15/ 01]</TH><TH ALIGN=RIGHT>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=hg38 hg38]</TH>
<TH ALIGN=RIGHT>455</TH>
  <TD ALIGN=RIGHT>3,209,286,105</TD><TD ALIGN=RIGHT>3,049,315,783</TD>
  <TD ALIGN=RIGHT>159,970,322</TD><TD ALIGN=RIGHT>%&nbsp;52.10</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>N/A</TH><TD ALIGN=RIGHT>N/A</TD>
<TD ALIGN=RIGHT>3000</TD>
  <TD ALIGN=CENTER>medium</TD></TR>
<TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/assembly/GCA_000696425.1/ 02]</TH><TH ALIGN=RIGHT>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=galVar1 galVar1]</TH>
<TH ALIGN=RIGHT>179,514</TH>
  <TD ALIGN=RIGHT>3,187,660,572</TD><TD ALIGN=RIGHT>2,802,837,430</TD>
  <TD ALIGN=RIGHT>384,823,142</TD><TD ALIGN=RIGHT>%&nbsp;38.66</TD>
  <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/assembly/GCF_000696425.1/ Malayan flying lemur]</TD><TH ALIGN=CENTER>55X</TH>
<TH ALIGN=CENTER>245189</TH>
  <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>57.036%</TD>
<TD ALIGN=RIGHT>3000</TD>
  <TD ALIGN=CENTER>medium</TD></TR>
<TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/assembly/GCA_000334495.1/ 03]</TH><TH ALIGN=RIGHT>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=tupChi1 tupChi1]</TH>
<TH ALIGN=RIGHT>50,750</TH>
  <TD ALIGN=RIGHT>2,846,580,235</TD><TD ALIGN=RIGHT>2,706,389,135</TD>
  <TD ALIGN=RIGHT>140,191,100</TD><TD ALIGN=RIGHT>%&nbsp;40.02</TD>
  <TD ALIGN=CENTER>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Tupaia_chinensis/TupChi_1.0/ Chinese tree shrew]</TD><TH ALIGN=CENTER>80X</TH>
<TH ALIGN=CENTER>3670124</TH>
  <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>45.256%</TD>
<TD ALIGN=RIGHT>3000</TD>
  <TD ALIGN=CENTER>medium</TD></TR>
<TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/genome/assembly/304568/ 04]</TH><TH ALIGN=RIGHT>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=cavPor3 cavPor3]</TH>
<TH ALIGN=RIGHT>3,144</TH>
  <TD ALIGN=RIGHT>2,723,219,641</TD><TD ALIGN=RIGHT>2,663,369,733</TD>
  <TD ALIGN=RIGHT>59,849,908</TD><TD ALIGN=RIGHT>%&nbsp;27.53</TD>
  <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AAKN02 Guinea pig]</TD><TH ALIGN=CENTER>6.76X</TH>
<TH ALIGN=CENTER>27942054</TH>
  <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>42.371%</TD>
<TD ALIGN=RIGHT>3000</TD>
  <TD ALIGN=CENTER>medium</TD></TR>
<TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/genome/assembly/327618/ 05]</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>SyntenicNet</TH><TD ALIGN=RIGHT>31.653%</TD>
<TD ALIGN=RIGHT>3000</TD>
  <TD ALIGN=CENTER>medium</TD></TR>
</TABLE>