Fr3 Genome size statistics: Difference between revisions

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(updated with chain net statistics accumulating)
(Updated hgwdev/genome-test links to .gi, all links validated)
 
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<UL>
<UL>
<LI>Fugu 6-way [[Fr3 conservation alignment]]</LI>
<LI>Fugu 8-way [[Fr3 conservation alignment]]</LI>
<LI>Fugu 6-way [[Fr3 conservation lastz parameters]]</LI>
<LI>Fugu 8-way [[Fr3 conservation lastz parameters]]</LI>
<LI>all other [[UCSC Multiple Alignments]]</LI>
<LI>all other [[UCSC Multiple Alignments]]</LI>
</UL>
</UL>
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   <TH>chain<BR>linearGap</TH>
   <TH>chain<BR>linearGap</TH>
<TR>
<TR>
<TR><TH ALIGN=RIGHT>[http://www.fugu-sg.org/ 01]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=fr3 fr3]</TH>
<TR><TH ALIGN=RIGHT>[http://www.fugu-sg.org/ 01]</TH><TH ALIGN=RIGHT>[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=fr3 fr3]</TH>
<TH ALIGN=RIGHT>6,835</TH>
<TH ALIGN=RIGHT>6,835</TH>
   <TD ALIGN=RIGHT>391,484,715</TD><TD ALIGN=RIGHT>350,961,831</TD>
   <TD ALIGN=RIGHT>391,484,715</TD><TD ALIGN=RIGHT>350,961,831</TD>
Line 47: Line 47:
<TD ALIGN=RIGHT>N/A</TD>
<TD ALIGN=RIGHT>N/A</TD>
   <TD ALIGN=CENTER>N/A</TD></TR>
   <TD ALIGN=CENTER>N/A</TD></TR>
<TR><TH ALIGN=RIGHT>[http://www.genoscope.cns.fr/spip/Tetraodon-nigroviridis-a-fish-with.html 02]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=tetNig2 tetNig2]</TH>
<TR><TH ALIGN=RIGHT>[http://www.genoscope.cns.fr/spip/Tetraodon-nigroviridis-a-fish-with.html 02]</TH><TH ALIGN=RIGHT>[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=tetNig2 tetNig2]</TH>
<TH ALIGN=RIGHT>27</TH>
<TH ALIGN=RIGHT>27</TH>
   <TD ALIGN=RIGHT>358,618,246</TD><TD ALIGN=RIGHT>302,314,788</TD>
   <TD ALIGN=RIGHT>358,618,246</TD><TD ALIGN=RIGHT>302,314,788</TD>
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<TD ALIGN=RIGHT>2000</TD>
<TD ALIGN=RIGHT>2000</TD>
   <TD ALIGN=CENTER>medium</TD></TR>
   <TD ALIGN=CENTER>medium</TD></TR>
<TR><TH ALIGN=RIGHT>[ftp://ftp.broadinstitute.org/pub/assemblies/fish/tilapia/Orenil1/ 03]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=oreNil1 oreNil1]</TH>
<TR><TH ALIGN=RIGHT>[ftp://ftp.broadinstitute.org/pub/assemblies/fish/tilapia/Orenil1/ 03]</TH><TH ALIGN=RIGHT>[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=oreNil1 oreNil1]</TH>
<TH ALIGN=RIGHT>5,901</TH>
<TH ALIGN=RIGHT>5,901</TH>
   <TD ALIGN=RIGHT>927,742,539</TD><TD ALIGN=RIGHT>816,084,674</TD>
   <TD ALIGN=RIGHT>927,742,539</TD><TD ALIGN=RIGHT>816,084,674</TD>
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<TD ALIGN=RIGHT>2000</TD>
<TD ALIGN=RIGHT>2000</TD>
   <TD ALIGN=CENTER>medium</TD></TR>
   <TD ALIGN=CENTER>medium</TD></TR>
<TR><TH ALIGN=RIGHT>[ftp://ftp.broadinstitute.org/pub/assemblies/fish/stickleback/gasAcu1/ 04]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=gasAcu1 gasAcu1]</TH>
<TR><TH ALIGN=RIGHT>[ftp://ftp.broadinstitute.org/pub/assemblies/fish/stickleback/gasAcu1/ 04]</TH><TH ALIGN=RIGHT>[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=gasAcu1 gasAcu1]</TH>
<TH ALIGN=RIGHT>23</TH>
<TH ALIGN=RIGHT>23</TH>
   <TD ALIGN=RIGHT>463,354,448</TD><TD ALIGN=RIGHT>446,627,861</TD>
   <TD ALIGN=RIGHT>463,354,448</TD><TD ALIGN=RIGHT>446,627,861</TD>
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   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AANH01 Stickleback]</TD><TH ALIGN=CENTER>6X</TH>
   <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>20083130</TH>
   <TH ALIGN=CENTER>in progress</TH><TD ALIGN=RIGHT>N/A</TD>
   <TH ALIGN=CENTER>Net</TH><TD ALIGN=RIGHT>55.527%</TD>
<TD ALIGN=RIGHT>1000</TD>
<TD ALIGN=RIGHT>2000</TD>
   <TD ALIGN=CENTER>N/A</TD></TR>
  <TD ALIGN=CENTER>medium</TD></TR>
<TR><TH ALIGN=RIGHT>[http://dolphin.lab.nig.ac.jp/medaka/index.php 05]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=oryLat2 oryLat2]</TH>
<TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/genome/2661 05]</TH><TH ALIGN=RIGHT>[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=gadMor1 gadMor1]</TH>
<TH ALIGN=RIGHT>427,428</TH>
  <TD ALIGN=RIGHT>824,327,835</TD><TD ALIGN=RIGHT>608,038,555</TD>
  <TD ALIGN=RIGHT>216,289,280</TD><TD ALIGN=RIGHT>%&nbsp;31.25</TD>
   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=CAEA00 Atlantic cod]</TD><TH ALIGN=CENTER>40X</TH>
<TH ALIGN=CENTER>393166</TH>
  <TH ALIGN=CENTER>Net</TH><TD ALIGN=RIGHT>30.327%</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-test.gi.ucsc.edu/cgi-bin/hgTracks?db=oryLat2 oryLat2]</TH>
<TH ALIGN=RIGHT>7,189</TH>
<TH ALIGN=RIGHT>7,189</TH>
   <TD ALIGN=RIGHT>869,000,216</TD><TD ALIGN=RIGHT>700,386,597</TD>
   <TD ALIGN=RIGHT>869,000,216</TD><TD ALIGN=RIGHT>700,386,597</TD>
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<TD ALIGN=RIGHT>2000</TD>
<TD ALIGN=RIGHT>2000</TD>
   <TD ALIGN=CENTER>medium</TD></TR>
   <TD ALIGN=CENTER>medium</TD></TR>
<TR><TH ALIGN=RIGHT>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_other/Danio_rerio/Zv9/ 06]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=danRer7 danRer7]</TH>
<TR><TH ALIGN=RIGHT>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_other/Danio_rerio/Zv9/ 07]</TH><TH ALIGN=RIGHT>[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=danRer7 danRer7]</TH>
<TH ALIGN=RIGHT>1,133</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>1,412,464,843</TD><TD ALIGN=RIGHT>1,409,770,109</TD>
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<TH ALIGN=CENTER>54093808</TH>
<TH ALIGN=CENTER>54093808</TH>
   <TH ALIGN=CENTER>Net</TH><TD ALIGN=RIGHT>22.823%</TD>
   <TH ALIGN=CENTER>Net</TH><TD ALIGN=RIGHT>22.823%</TD>
<TD ALIGN=RIGHT>2000</TD>
  <TD ALIGN=CENTER>medium</TD></TR>
<TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/bioproject/56111 08]</TH><TH ALIGN=RIGHT>[http://genome-test.gi.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>13.735%</TD>
<TD ALIGN=RIGHT>2000</TD>
<TD ALIGN=RIGHT>2000</TD>
   <TD ALIGN=CENTER>medium</TD></TR>
   <TD ALIGN=CENTER>medium</TD></TR>
</TABLE>
</TABLE>

Latest revision as of 21:37, 30 August 2018

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-test		 chrom
count		 total
size		 non-N
bases		 N base
count		 % masked common name/
src info		 coverage N50
chrom.sizes		 alignment type % of fr3
matched
(chainLink table)		 chain
minScore		 chain
linearGap
01fr3 6,835 391,484,715350,961,831 40,522,884% 19.01 Fugu8.5X 11516971 N/AN/A N/A N/A
02tetNig2 27 358,618,246302,314,788 56,303,458% 20.27 Tetraodon7.9X 13390619 Net70.912% 2000 medium
03oreNil1 5,901 927,742,539816,084,674 111,657,865% 25.51 Nile tilapia269X 2802423 Net57.240% 2000 medium
04gasAcu1 23 463,354,448446,627,861 16,726,587% 2.58 Stickleback6X 20083130 Net55.527% 2000 medium
05gadMor1 427,428 824,327,835608,038,555 216,289,280% 31.25 Atlantic cod40X 393166 Net30.327% 2000 medium
06oryLat2 7,189 869,000,216700,386,597 168,613,619% 33.09 Medaka10.6X 29908082 Net43.863% 2000 medium
07danRer7 1,133 1,412,464,8431,409,770,109 2,694,734% 52.06 Zebrafish30X 54093808 Net22.823% 2000 medium
08latCha1 22,819 2,860,591,9212,183,592,768 676,999,153% 45.68 Coelacanth77.5X 924513 Net13.735% 2000 medium
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