Ce10 Genome size statistics: Difference between revisions

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<UL>
<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>
<LI>all other [[UCSC Multiple Alignments]]</LI>
</UL>
</UL>
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==do not edit, automatically generated table==
==do not edit, automatically generated table==


<TABLE BORDER=1>
<TABLE BORDER=1>
<TR><TH>order<BR>count/<BR>ftp&nbsp;src</TH>
<TR><TH>order<BR>count/<BR>ftp&nbsp;src</TH>
   <TH>ucsc<BR>db&nbsp;name/<BR>src&nbsp;info</TH>
   <TH>ucsc<BR>db&nbsp;name/<BR>genome-preview</TH>
   <TH>chrom<BR>count</TH>
   <TH>chrom<BR>count</TH>
   <TH>total<BR>size</TH>
   <TH>total<BR>size</TH>
Line 28: Line 31:
   <TH>N&nbsp;base<BR>count</TH>
   <TH>N&nbsp;base<BR>count</TH>
   <TH>%&nbsp;masked</TH>
   <TH>%&nbsp;masked</TH>
   <TH>common&nbsp;name/<BR>genome-test</TH>
   <TH>common&nbsp;name/<BR>src&nbsp;info</TH>
   <TH>coverage</TH>
   <TH>coverage</TH>
   <TH>N50<BR>chrom.sizes</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>
<TR><TH ALIGN=RIGHT>[ftp://ftp.sanger.ac.uk/pub/wormbase/WS220/genomes/c_elegans/ 01]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=ce10 ce10]</TH>
<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>
<TH ALIGN=RIGHT>7</TH>
   <TD ALIGN=RIGHT>100,286,070</TD><TD ALIGN=RIGHT>100,286,070</TD>
   <TD ALIGN=RIGHT>100,286,070</TD><TD ALIGN=RIGHT>100,286,070</TD>
Line 38: Line 45:
   <TD ALIGN=CENTER>[http://wiki.wormbase.org/index.php/Caenorhabditis_elegans C. elegans]</TD><TH ALIGN=CENTER>30X</TH>
   <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>17493793</TH>
<TR><TH ALIGN=RIGHT>[ftp://ftp.sanger.ac.uk/pub/wormbase/WS225/genomes/c_briggsae/ 02]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=cb4 cb4]</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>
<TH ALIGN=RIGHT>13</TH>
   <TD ALIGN=RIGHT>108,434,085</TD><TD ALIGN=RIGHT>105,430,959</TD>
   <TD ALIGN=RIGHT>108,434,085</TD><TD ALIGN=RIGHT>105,430,959</TD>
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   <TD ALIGN=CENTER>[http://www.sanger.ac.uk/Projects/C_briggsae/ C. briggsae]</TD><TH ALIGN=CENTER>10X</TH>
   <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>17485439</TH>
<TR><TH ALIGN=RIGHT>[ftp://ftp.sanger.ac.uk/pub/wormbase/WS220/genomes/c_remanei/ 03]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=caeRem4 caeRem4]</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>
<TH ALIGN=RIGHT>3,670</TH>
   <TD ALIGN=RIGHT>145,442,736</TD><TD ALIGN=RIGHT>138,406,203</TD>
   <TD ALIGN=RIGHT>145,442,736</TD><TD ALIGN=RIGHT>138,406,203</TD>
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   <TD ALIGN=CENTER>[http://genome.wustl.edu/genomes/view/caenorhabditis_remanei/ C. remanei]</TD><TH ALIGN=CENTER>9.2X</TH>
   <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>435512</TH>
<TR><TH ALIGN=RIGHT>[ftp://ftp.sanger.ac.uk/pub/wormbase/WS220/genomes/c_brenneri/ 04]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=caePb3 caePb3]</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>
<TH ALIGN=RIGHT>3,307</TH>
   <TD ALIGN=RIGHT>190,374,847</TD><TD ALIGN=RIGHT>170,097,428</TD>
   <TD ALIGN=RIGHT>190,374,847</TD><TD ALIGN=RIGHT>170,097,428</TD>
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   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ABEG02 C. brenneri]</TD><TH ALIGN=CENTER>9.5X</TH>
   <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>381961</TH>
<TR><TH ALIGN=RIGHT>[ftp://ftp.sanger.ac.uk/pub/wormbase/WS220/genomes/c_japonica/ 05]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=caeJap4 caeJap4]</TH>
  <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>40.644%</TD>
<TH ALIGN=RIGHT>7,552</TH>
<TD ALIGN=RIGHT>1000</TD>
  <TD ALIGN=RIGHT>163,161,801</TD><TD ALIGN=RIGHT>129,321,631</TD>
   <TD ALIGN=CENTER>loose</TD></TR>
  <TD ALIGN=RIGHT>33,840,170</TD><TD ALIGN=RIGHT>%&nbsp;44.50</TD>
<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>
   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ABLE03 C. japonica]</TD><TH ALIGN=CENTER>22X</TH>
<TH ALIGN=CENTER>90117</TH>
<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/ 06]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=caeSp71 caeSp71]</TH>
<TH ALIGN=RIGHT>52,546</TH>
<TH ALIGN=RIGHT>52,546</TH>
   <TD ALIGN=RIGHT>196,410,749</TD><TD ALIGN=RIGHT>177,605,791</TD>
   <TD ALIGN=RIGHT>196,410,749</TD><TD ALIGN=RIGHT>177,605,791</TD>
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   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AENL01 C. sp. 7 ju1286]</TD><TH ALIGN=CENTER>37.9X</TH>
   <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>73785</TH>
<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/ 07]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=caeSp91 caeSp91]</TH>
  <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>40.236%</TD>
<TH ALIGN=RIGHT>7,636</TH>
<TD ALIGN=RIGHT>1000</TD>
   <TD ALIGN=RIGHT>204,396,809</TD><TD ALIGN=RIGHT>186,540,270</TD>
  <TD ALIGN=CENTER>loose</TD></TR>
   <TD ALIGN=RIGHT>17,856,539</TD><TD ALIGN=RIGHT>%&nbsp;31.67</TD>
<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>
   <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=RIGHT>18,817</TH>
<TH ALIGN=CENTER>196652</TH>
   <TD ALIGN=RIGHT>166,256,191</TD><TD ALIGN=RIGHT>154,057,934</TD>
<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/ 08]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=caeSp111 caeSp111]</TH>
   <TD ALIGN=RIGHT>12,198,257</TD><TD ALIGN=RIGHT>%&nbsp;46.77</TD>
<TH ALIGN=RIGHT>665</TH>
   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ABLE03 C. japonica]</TD><TH ALIGN=CENTER>22X</TH>
  <TD ALIGN=RIGHT>79,321,433</TD><TD ALIGN=RIGHT>76,497,192</TD>
<TH ALIGN=CENTER>94149</TH>
  <TD ALIGN=RIGHT>2,824,241</TD><TD ALIGN=RIGHT>%&nbsp;29.15</TD>
  <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>27.737%</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>
<TD ALIGN=RIGHT>1000</TD>
<TH ALIGN=CENTER>20921866</TH>
   <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-test.cse.ucsc.edu/cgi-bin/hgTracks?db=caeAng1 caeAng1]</TH>
<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>
<TH ALIGN=RIGHT>33,559</TH>
   <TD ALIGN=RIGHT>79,761,545</TD><TD ALIGN=RIGHT>75,258,781</TD>
   <TD ALIGN=RIGHT>79,761,545</TD><TD ALIGN=RIGHT>75,258,781</TD>
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   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AEHI01 C. angaria]</TD><TH ALIGN=CENTER>170X</TH>
   <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>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>
</TABLE>

Latest revision as of 23:20, 10 June 2011

see also

statistics collected from UCSC 2bit files

  • The external link in the first column goes to the FTP location where the genome sequence was obtained
  • The external links from the UCSC database name go to the UCSC genome-test browser for that genome
  • N bases == unknown bases in the assembly marked by "N"
  • non-N bases == called bases in the assembly
  • total size == all bases in assembly, N and non-N
  • The % masked is masking from Repeat Masker or Window Masker plus TRF/Simple Repeats, whichever is greater, usually WindowMasker for these genomes
  • The common name external links go to information pages for this genome
  • The coverage numbers are taken directly from information README files from the sequencing center
  • 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

do not edit, automatically generated table

order
count/
ftp src		 ucsc
db name/
genome-preview		 chrom
count		 total
size		 non-N
bases		 N base
count		 % masked common name/
src info		 coverage N50
chrom.sizes		 alignment type % of ce10
matched
(chainLink table)		 chain
minScore		 chain
linearGap
01ce10 7 100,286,070100,286,070 0% 13.38 C. elegans30X 17493793 N/AN/A 1000 N/A
02cb4 13 108,434,085105,430,959 3,003,126% 36.52 C. briggsae10X 17485439 SyntenicNet39.386% 1000 loose
03caeSp91 7,636 204,396,809186,540,270 17,856,539% 31.67 C. sp. 9 ju142237.6X 196652 SyntenicNet42.169% 1000 loose
04caeRem4 3,670 145,442,736138,406,203 7,036,533% 30.48 C. remanei9.2X 435512 SyntenicNet41.722% 1000 loose
05caeSp111 665 79,321,43376,497,192 2,824,241% 29.15 C. sp. 11 ju137320.2X 20921866 SyntenicNet37.876% 1000 loose
06caePb3 3,307 190,374,847170,097,428 20,277,419% 29.30 C. brenneri9.5X 381961 SyntenicNet40.644% 1000 loose
07caeSp71 52,546 196,410,749177,605,791 18,804,958% 31.53 C. sp. 7 ju128637.9X 73785 SyntenicNet40.236% 1000 loose
08caeJap4 18,817 166,256,191154,057,934 12,198,257% 46.77 C. japonica22X 94149 SyntenicNet27.737% 1000 loose
09caeAng1 33,559 79,761,54575,258,781 4,502,764% 38.31 C. angaria170X 9453 SyntenicNet17.625% 1000 loose
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