GorGor3 Genome size statistics: Difference between revisions

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(initial contents from sizeStats.pl)
 
(Updated hgwdev/genome-test links to .gi, links validated)
 
Line 38: Line 38:
   <TH>chain<BR>linearGap</TH>
   <TH>chain<BR>linearGap</TH>
<TR>
<TR>
<TR><TH ALIGN=RIGHT>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Gorilla_gorilla/gorGor3.1/ 01]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=gorGor3 gorGor3]</TH>
<TR><TH ALIGN=RIGHT>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Gorilla_gorilla/gorGor3.1/ 01]</TH><TH ALIGN=RIGHT>[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=gorGor3 gorGor3]</TH>
<TH ALIGN=RIGHT>46,823</TH>
<TH ALIGN=RIGHT>46,823</TH>
   <TD ALIGN=RIGHT>3,029,553,646</TD><TD ALIGN=RIGHT>2,822,760,080</TD>
   <TD ALIGN=RIGHT>3,029,553,646</TD><TD ALIGN=RIGHT>2,822,760,080</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://genome.wustl.edu/genomes/view/pan_troglodytes/ 02]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=panTro3 panTro3]</TH>
<TR><TH ALIGN=RIGHT>[http://genome.wustl.edu/genomes/view/pan_troglodytes/ 02]</TH><TH ALIGN=RIGHT>[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=panTro3 panTro3]</TH>
<TH ALIGN=RIGHT>24,132</TH>
<TH ALIGN=RIGHT>24,132</TH>
   <TD ALIGN=RIGHT>3,307,960,432</TD><TD ALIGN=RIGHT>2,900,529,764</TD>
   <TD ALIGN=RIGHT>3,307,960,432</TD><TD ALIGN=RIGHT>2,900,529,764</TD>
Line 56: Line 56:
<TD ALIGN=RIGHT>5000</TD>
<TD ALIGN=RIGHT>5000</TD>
   <TD ALIGN=CENTER>medium</TD></TR>
   <TD ALIGN=CENTER>medium</TD></TR>
<TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/data/index.shtml 03]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=hg19 hg19]</TH>
<TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/data/index.shtml 03]</TH><TH ALIGN=RIGHT>[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=hg19 hg19]</TH>
<TH ALIGN=RIGHT>93</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>3,137,161,264</TD><TD ALIGN=RIGHT>2,897,310,462</TD>
Line 65: Line 65:
<TD ALIGN=RIGHT>5000</TD>
<TD ALIGN=RIGHT>5000</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_mammals/Nomascus_leucogenys/Nleu1.0/ 04]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=nomLeu1 nomLeu1]</TH>
<TR><TH ALIGN=RIGHT>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Nomascus_leucogenys/Nleu1.0/ 04]</TH><TH ALIGN=RIGHT>[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=nomLeu1 nomLeu1]</TH>
<TH ALIGN=RIGHT>17,968</TH>
<TH ALIGN=RIGHT>17,968</TH>
   <TD ALIGN=RIGHT>2,936,035,333</TD><TD ALIGN=RIGHT>2,756,591,777</TD>
   <TD ALIGN=RIGHT>2,936,035,333</TD><TD ALIGN=RIGHT>2,756,591,777</TD>
Line 74: Line 74:
<TD ALIGN=RIGHT>5000</TD>
<TD ALIGN=RIGHT>5000</TD>
   <TD ALIGN=CENTER>medium</TD></TR>
   <TD ALIGN=CENTER>medium</TD></TR>
<TR><TH ALIGN=RIGHT>[http://genome.wustl.edu/genomes/view/pongo_abelii/ 05]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=ponAbe2 ponAbe2]</TH>
<TR><TH ALIGN=RIGHT>[http://genome.wustl.edu/genomes/view/pongo_abelii/ 05]</TH><TH ALIGN=RIGHT>[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=ponAbe2 ponAbe2]</TH>
<TH ALIGN=RIGHT>55</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>3,446,771,396</TD><TD ALIGN=RIGHT>3,093,543,172</TD>
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<TD ALIGN=RIGHT>5000</TD>
<TD ALIGN=RIGHT>5000</TD>
   <TD ALIGN=CENTER>medium</TD></TR>
   <TD ALIGN=CENTER>medium</TD></TR>
<TR><TH ALIGN=RIGHT>[http://www.hgsc.bcm.tmc.edu/project-species-p-Papio%20hamadryas.hgsc?pageLocation=Papio%20hamadryas 06]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=papHam1 papHam1]</TH>
<TR><TH ALIGN=RIGHT>[http://www.hgsc.bcm.tmc.edu/project-species-p-Papio%20hamadryas.hgsc?pageLocation=Papio%20hamadryas 06]</TH><TH ALIGN=RIGHT>[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=papHam1 papHam1]</TH>
<TH ALIGN=RIGHT>387,374</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>2,867,564,654</TD><TD ALIGN=RIGHT>2,741,849,051</TD>
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<TD ALIGN=RIGHT>5000</TD>
<TD ALIGN=RIGHT>5000</TD>
   <TD ALIGN=CENTER>medium</TD></TR>
   <TD ALIGN=CENTER>medium</TD></TR>
<TR><TH ALIGN=RIGHT>[http://www.hgsc.bcm.tmc.edu/project-species-p-Rhesus%20Macaque.hgsc?pageLocation=Rhesus%20Macaque 07]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=rheMac2 rheMac2]</TH>
<TR><TH ALIGN=RIGHT>[http://www.hgsc.bcm.tmc.edu/project-species-p-Rhesus%20Macaque.hgsc?pageLocation=Rhesus%20Macaque 07]</TH><TH ALIGN=RIGHT>[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=rheMac2 rheMac2]</TH>
<TH ALIGN=RIGHT>22</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>2,864,106,071</TD><TD ALIGN=RIGHT>2,646,668,809</TD>
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<TD ALIGN=RIGHT>5000</TD>
<TD ALIGN=RIGHT>5000</TD>
   <TD ALIGN=CENTER>medium</TD></TR>
   <TD ALIGN=CENTER>medium</TD></TR>
<TR><TH ALIGN=RIGHT>[http://genome.wustl.edu/genomes/view/callithrix_jacchus/ 08]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=calJac3 calJac3]</TH>
<TR><TH ALIGN=RIGHT>[http://genome.wustl.edu/genomes/view/callithrix_jacchus/ 08]</TH><TH ALIGN=RIGHT>[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=calJac3 calJac3]</TH>
<TH ALIGN=RIGHT>14,205</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>2,914,958,544</TD><TD ALIGN=RIGHT>2,752,505,800</TD>
Line 110: Line 110:
<TD ALIGN=RIGHT>5000</TD>
<TD ALIGN=RIGHT>5000</TD>
   <TD ALIGN=CENTER>medium</TD></TR>
   <TD ALIGN=CENTER>medium</TD></TR>
<TR><TH ALIGN=RIGHT>[ftp://ftp.broad.mit.edu/pub/assemblies/mammals/tarsier/Tarsyr1.0/ 09]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=tarSyr1 tarSyr1]</TH>
<TR><TH ALIGN=RIGHT>[ftp://ftp.broad.mit.edu/pub/assemblies/mammals/tarsier/Tarsyr1.0/ 09]</TH><TH ALIGN=RIGHT>[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=tarSyr1 tarSyr1]</TH>
<TH ALIGN=RIGHT>656,709</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>3,179,905,132</TD><TD ALIGN=RIGHT>2,768,536,343</TD>
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<TD ALIGN=RIGHT>5000</TD>
<TD ALIGN=RIGHT>5000</TD>
   <TD ALIGN=CENTER>medium</TD></TR>
   <TD ALIGN=CENTER>medium</TD></TR>
<TR><TH ALIGN=RIGHT>[http://www.broadinstitute.org/ftp/pub/assemblies/mammals/mouseLemur/MicMur1.0/ 10]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=micMur1 micMur1]</TH>
<TR><TH ALIGN=RIGHT>[http://www.broadinstitute.org/ftp/pub/assemblies/mammals/mouseLemur/MicMur1.0/ 10]</TH><TH ALIGN=RIGHT>[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=micMur1 micMur1]</TH>
<TH ALIGN=RIGHT>185,042</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>2,902,270,736</TD><TD ALIGN=RIGHT>1,852,394,361</TD>
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<TD ALIGN=RIGHT>5000</TD>
<TD ALIGN=RIGHT>5000</TD>
   <TD ALIGN=CENTER>medium</TD></TR>
   <TD ALIGN=CENTER>medium</TD></TR>
<TR><TH ALIGN=RIGHT>[http://www.broadinstitute.org/ftp/pub/assemblies/mammals/bushbaby/otoGar1/ 11]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=otoGar1 otoGar1]</TH>
<TR><TH ALIGN=RIGHT>[http://www.broadinstitute.org/ftp/pub/assemblies/mammals/bushbaby/otoGar1/ 11]</TH><TH ALIGN=RIGHT>[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=otoGar1 otoGar1]</TH>
<TH ALIGN=RIGHT>120,882</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>3,420,058,864</TD><TD ALIGN=RIGHT>1,969,052,059</TD>

Latest revision as of 00:21, 1 September 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 gorGor3
matched
(chainLink table)		 chain
minScore		 chain
linearGap
01gorGor3 46,823 3,029,553,6462,822,760,080 206,793,566% 48.80 Gorilla2.1X 145327772 N/AN/A N/A N/A
02panTro3 24,132 3,307,960,4322,900,529,764 407,430,668% 50.64 Chimp6X 143986469 Net89.043% 5000 medium
03hg19 93 3,137,161,2642,897,310,462 239,850,802% 50.63 Human20X 146364022 Net91.109% 5000 medium
04nomLeu1 17,968 2,936,035,3332,756,591,777 179,443,556% 50.82 Gibbon5.6X 22692035 Net83.476% 5000 medium
05ponAbe2 55 3,446,771,3963,093,543,172 353,228,224% 50.89 Orangutan6X 135191526 Net86.354% 5000 medium
06papHam1 387,374 2,867,564,6542,741,849,051 125,715,603% 48.70 Baboon5.3X 88525 Net79.434% 5000 medium
07rheMac2 22 2,864,106,0712,646,668,809 217,437,262% 48.28 Rhesus5.1X 153947521 Net79.244% 5000 medium
08calJac3 14,205 2,914,958,5442,752,505,800 162,452,744% 47.71 Marmoset6X 132174527 Net68.507% 5000 medium
09tarSyr1 656,709 3,179,905,1322,768,536,343 411,368,789% 41.75 Tarsier2X 12214 Net19.482% 5000 medium
10micMur1 185,042 2,902,270,7361,852,394,361 1,049,876,375% 37.31 Mouse lemur2X 140884 Net22.908% 5000 medium
11otoGar1 120,882 3,420,058,8641,969,052,059 1,451,006,805% 34.89 Bushbaby2X 139426 Net12.017% 5000 medium
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