XenTro3 Genome size statistics: Difference between revisions

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(fixing galGal3 reference)
(forgot to include xenTro3)
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<LI>X. tropicalis 8-way [[XenTro3 conservation alignment]]</LI>
<LI>X. tropicalis 8-way [[XenTro3 conservation alignment]]</LI>
<LI>X. tropicalis 8-way [[XenTro3 conservation lastz parameters]]</LI>
<LI>X. tropicalis 8-way [[XenTro3 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-test 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>
==see also==
<UL>
<LI>X. tropicalis 9-way [[XenTro3 conservation alignment]]</LI>
<LI>X. tropicalis 9-way [[XenTro3 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>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_other/Anolis_carolinensis/ 01]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=anoCar2 anoCar2]</TH>
<TR><TH ALIGN=RIGHT>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_other/Xenopus_tropicalis/v4.2/ 01]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=xenTro3 xenTro3]</TH>
<TH ALIGN=RIGHT>19,550</TH>
  <TD ALIGN=RIGHT>1,511,735,326</TD><TD ALIGN=RIGHT>1,358,334,882</TD>
  <TD ALIGN=RIGHT>153,400,444</TD><TD ALIGN=RIGHT>%&nbsp;24.55</TD>
  <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AAMC01 X. tropicalis]</TD><TH ALIGN=CENTER>7.65X</TH>
<TH ALIGN=CENTER>1567461</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.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_other/Anolis_carolinensis/ 02]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=anoCar2 anoCar2]</TH>
<TH ALIGN=RIGHT>6,457</TH>
<TH ALIGN=RIGHT>6,457</TH>
   <TD ALIGN=RIGHT>1,799,143,587</TD><TD ALIGN=RIGHT>1,701,353,767</TD>
   <TD ALIGN=RIGHT>1,799,143,587</TD><TD ALIGN=RIGHT>1,701,353,767</TD>
Line 68: Line 98:
<TD ALIGN=RIGHT>5000</TD>
<TD ALIGN=RIGHT>5000</TD>
   <TD ALIGN=CENTER>loose</TD></TR>
   <TD ALIGN=CENTER>loose</TD></TR>
<TR><TH ALIGN=RIGHT>[http://genome.wustl.edu/pub/organism/Other_Vertebrates/Gallus_gallus/assembly/Gallus_gallus-3.0/ 02]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=galGal3 galGal3]</TH>
<TR><TH ALIGN=RIGHT>[http://genome.wustl.edu/pub/organism/Other_Vertebrates/Gallus_gallus/assembly/Gallus_gallus-3.0/ 03]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=galGal3 galGal3]</TH>
<TH ALIGN=RIGHT>57</TH>
<TH ALIGN=RIGHT>57</TH>
   <TD ALIGN=RIGHT>1,100,480,441</TD><TD ALIGN=RIGHT>1,042,583,135</TD>
   <TD ALIGN=RIGHT>1,100,480,441</TD><TD ALIGN=RIGHT>1,042,583,135</TD>
Line 77: Line 107:
<TD ALIGN=RIGHT>5000</TD>
<TD ALIGN=RIGHT>5000</TD>
   <TD ALIGN=CENTER>loose</TD></TR>
   <TD ALIGN=CENTER>loose</TD></TR>
<TR><TH ALIGN=RIGHT>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_other/Meleagris_gallopavo/Turkey_2.01/ 03]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=melGal1 melGal1]</TH>
<TR><TH ALIGN=RIGHT>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_other/Meleagris_gallopavo/Turkey_2.01/ 04]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=melGal1 melGal1]</TH>
<TH ALIGN=RIGHT>5,891</TH>
<TH ALIGN=RIGHT>5,891</TH>
   <TD ALIGN=RIGHT>1,061,817,101</TD><TD ALIGN=RIGHT>935,922,386</TD>
   <TD ALIGN=RIGHT>1,061,817,101</TD><TD ALIGN=RIGHT>935,922,386</TD>
Line 86: Line 116:
<TD ALIGN=RIGHT>5000</TD>
<TD ALIGN=RIGHT>5000</TD>
   <TD ALIGN=CENTER>loose</TD></TR>
   <TD ALIGN=CENTER>loose</TD></TR>
<TR><TH ALIGN=RIGHT>[http://www.broadinstitute.org/mammals/opossum 04]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=monDom5 monDom5]</TH>
<TR><TH ALIGN=RIGHT>[http://www.broadinstitute.org/mammals/opossum 05]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=monDom5 monDom5]</TH>
<TH ALIGN=RIGHT>11</TH>
<TH ALIGN=RIGHT>11</TH>
   <TD ALIGN=RIGHT>3,605,631,728</TD><TD ALIGN=RIGHT>3,501,660,299</TD>
   <TD ALIGN=RIGHT>3,605,631,728</TD><TD ALIGN=RIGHT>3,501,660,299</TD>
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<TD ALIGN=RIGHT>5000</TD>
<TD ALIGN=RIGHT>5000</TD>
   <TD ALIGN=CENTER>loose</TD></TR>
   <TD ALIGN=CENTER>loose</TD></TR>
<TR><TH ALIGN=RIGHT>[http://www.hgsc.bcm.tmc.edu/project-species-m-Rat.hgsc?pageLocation=Rat 05]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=rn4 rn4]</TH>
<TR><TH ALIGN=RIGHT>[http://www.hgsc.bcm.tmc.edu/project-species-m-Rat.hgsc?pageLocation=Rat 06]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=rn4 rn4]</TH>
<TH ALIGN=RIGHT>45</TH>
<TH ALIGN=RIGHT>45</TH>
   <TD ALIGN=RIGHT>2,834,127,293</TD><TD ALIGN=RIGHT>2,566,294,765</TD>
   <TD ALIGN=RIGHT>2,834,127,293</TD><TD ALIGN=RIGHT>2,566,294,765</TD>
Line 104: Line 134:
<TD ALIGN=RIGHT>5000</TD>
<TD ALIGN=RIGHT>5000</TD>
   <TD ALIGN=CENTER>loose</TD></TR>
   <TD ALIGN=CENTER>loose</TD></TR>
<TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/mouse/index.shtml 06]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=mm9 mm9]</TH>
<TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/mouse/index.shtml 07]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=mm9 mm9]</TH>
<TH ALIGN=RIGHT>35</TH>
<TH ALIGN=RIGHT>35</TH>
   <TD ALIGN=RIGHT>2,725,765,481</TD><TD ALIGN=RIGHT>2,620,345,972</TD>
   <TD ALIGN=RIGHT>2,725,765,481</TD><TD ALIGN=RIGHT>2,620,345,972</TD>
Line 113: Line 143:
<TD ALIGN=RIGHT>5000</TD>
<TD ALIGN=RIGHT>5000</TD>
   <TD ALIGN=CENTER>loose</TD></TR>
   <TD ALIGN=CENTER>loose</TD></TR>
<TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/data/index.shtml 07]</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 08]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.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 122: Line 152:
<TD ALIGN=RIGHT>5000</TD>
<TD ALIGN=RIGHT>5000</TD>
   <TD ALIGN=CENTER>loose</TD></TR>
   <TD ALIGN=CENTER>loose</TD></TR>
<TR><TH ALIGN=RIGHT>[http://www.sanger.ac.uk/Projects/D_rerio/Zv9_assembly_information.shtml 08]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=danRer7 danRer7]</TH>
<TR><TH ALIGN=RIGHT>[http://www.sanger.ac.uk/Projects/D_rerio/Zv9_assembly_information.shtml 09]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.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>

Revision as of 23:45, 23 September 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

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

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 xenTro3
matched
(chainLink table)		 chain
minScore		 chain
linearGap
01xenTro3 19,550 1,511,735,3261,358,334,882 153,400,444% 24.55 X. tropicalis7.65X 1567461 N/AN/A N/A N/A
02anoCar2 6,457 1,799,143,5871,701,353,767 97,789,820% 41.98 Lizard7.1X 150641573 Net6.775% 5000 loose
03galGal3 57 1,100,480,4411,042,583,135 57,897,306% 9.85 Chicken6.6X 94230402 Net4.730% 5000 loose
04melGal1 5,891 1,061,817,101935,922,386 125,894,715% 0.00 Turkey5X 74864452 Net3.120% 5000 loose
05monDom5 11 3,605,631,7283,501,660,299 103,971,429% 55.95 Opossum6.8X 527952102 Net5.492% 5000 loose
06rn4 45 2,834,127,2932,566,294,765 267,832,528% 44.29 Rat20X 143002779 Net5.216% 5000 loose
07mm9 35 2,725,765,4812,620,345,972 105,419,509% 44.09 Mouse20X 131738871 Net6.609% 5000 loose
08hg19 93 3,137,161,2642,897,310,462 239,850,802% 50.63 Human20X 146364022 Net6.694% 5000 loose
09danRer7 1,133 1,412,464,8431,409,770,109 2,694,734% 52.06 Zebrafish30X 54093808 Net7.107% 5000 loose
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