Fr3 Genome size statistics: Difference between revisions

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(initial contents)
 
(updated with chain net statistics accumulating)
Line 53: Line 53:
   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=CAAE01 Tetraodon]</TD><TH ALIGN=CENTER>7.9X</TH>
   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=CAAE01 Tetraodon]</TD><TH ALIGN=CENTER>7.9X</TH>
<TH ALIGN=CENTER>13390619</TH>
<TH ALIGN=CENTER>13390619</TH>
   <TH ALIGN=CENTER>N/A</TH><TD ALIGN=RIGHT>N/A</TD>
   <TH ALIGN=CENTER>Net</TH><TD ALIGN=RIGHT>70.912%</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>[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.cse.ucsc.edu/cgi-bin/hgTracks?db=oreNil1 oreNil1]</TH>
<TH ALIGN=RIGHT>5,901</TH>
<TH ALIGN=RIGHT>5,901</TH>
Line 62: Line 62:
   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AERX01 Nile tilapia]</TD><TH ALIGN=CENTER>269X</TH>
   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AERX01 Nile tilapia]</TD><TH ALIGN=CENTER>269X</TH>
<TH ALIGN=CENTER>2802423</TH>
<TH ALIGN=CENTER>2802423</TH>
   <TH ALIGN=CENTER>N/A</TH><TD ALIGN=RIGHT>N/A</TD>
   <TH ALIGN=CENTER>Net</TH><TD ALIGN=RIGHT>57.240%</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>[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.cse.ucsc.edu/cgi-bin/hgTracks?db=gasAcu1 gasAcu1]</TH>
<TH ALIGN=RIGHT>23</TH>
<TH ALIGN=RIGHT>23</TH>
Line 71: Line 71:
   <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>N/A</TH><TD ALIGN=RIGHT>N/A</TD>
   <TH ALIGN=CENTER>in progress</TH><TD ALIGN=RIGHT>N/A</TD>
<TD ALIGN=RIGHT>1000</TD>
<TD ALIGN=RIGHT>1000</TD>
   <TD ALIGN=CENTER>N/A</TD></TR>
   <TD ALIGN=CENTER>N/A</TD></TR>
Line 80: Line 80:
   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=BAAE01 Medaka]</TD><TH ALIGN=CENTER>10.6X</TH>
   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=BAAE01 Medaka]</TD><TH ALIGN=CENTER>10.6X</TH>
<TH ALIGN=CENTER>29908082</TH>
<TH ALIGN=CENTER>29908082</TH>
   <TH ALIGN=CENTER>N/A</TH><TD ALIGN=RIGHT>N/A</TD>
   <TH ALIGN=CENTER>Net</TH><TD ALIGN=RIGHT>43.863%</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>[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/ 06]</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>
Line 89: Line 89:
   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=CABZ00 Zebrafish]</TD><TH ALIGN=CENTER>30X</TH>
   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=CABZ00 Zebrafish]</TD><TH ALIGN=CENTER>30X</TH>
<TH ALIGN=CENTER>54093808</TH>
<TH ALIGN=CENTER>54093808</TH>
   <TH ALIGN=CENTER>N/A</TH><TD ALIGN=RIGHT>N/A</TD>
   <TH ALIGN=CENTER>Net</TH><TD ALIGN=RIGHT>22.823%</TD>
<TD ALIGN=RIGHT>1000</TD>
<TD ALIGN=RIGHT>2000</TD>
   <TD ALIGN=CENTER>N/A</TD></TR>
   <TD ALIGN=CENTER>medium</TD></TR>
</TABLE>
</TABLE>

Revision as of 19:04, 2 December 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-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 in progressN/A 1000 N/A
05oryLat2 7,189 869,000,216700,386,597 168,613,619% 33.09 Medaka10.6X 29908082 Net43.863% 2000 medium
06danRer7 1,133 1,412,464,8431,409,770,109 2,694,734% 52.06 Zebrafish30X 54093808 Net22.823% 2000 medium
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