DanRer7 Genome size statistics: Difference between revisions

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(fixup mm9 and hg19)
Line 48: Line 48:
<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>N/A</TH><TD ALIGN=RIGHT>N/A</TD>
<TD ALIGN=RIGHT>1000</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>02</TH><TH ALIGN=RIGHT>[ftp://ftp.broad.mit.edu/pub/assemblies/fish/stickleback/gasAcu1/ gasAcu1]</TH>
<TR><TH ALIGN=RIGHT>02</TH><TH ALIGN=RIGHT>[ftp://ftp.broad.mit.edu/pub/assemblies/fish/stickleback/gasAcu1/ gasAcu1]</TH>
Line 56: Line 56:
   <TD ALIGN=CENTER>Stickleback</TD><TH ALIGN=CENTER>6X</TH>
   <TD ALIGN=CENTER>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>10.270%</TD>
   <TH ALIGN=CENTER>MAF net</TH><TD ALIGN=RIGHT>10.270%</TD>
<TD ALIGN=RIGHT>2000</TD>
<TD ALIGN=RIGHT>2000</TD>
   <TD ALIGN=CENTER>medium</TD></TR>
   <TD ALIGN=CENTER>medium</TD></TR>
Line 65: Line 65:
   <TD ALIGN=CENTER>Medaka</TD><TH ALIGN=CENTER>10.6X</TH>
   <TD ALIGN=CENTER>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>10.032%</TD>
   <TH ALIGN=CENTER>MAF net</TH><TD ALIGN=RIGHT>10.032%</TD>
<TD ALIGN=RIGHT>2000</TD>
<TD ALIGN=RIGHT>2000</TD>
   <TD ALIGN=CENTER>medium</TD></TR>
   <TD ALIGN=CENTER>medium</TD></TR>
Line 74: Line 74:
   <TD ALIGN=CENTER>Tetraodon</TD><TH ALIGN=CENTER>7.9X</TH>
   <TD ALIGN=CENTER>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>6.273%</TD>
   <TH ALIGN=CENTER>MAF net</TH><TD ALIGN=RIGHT>6.273%</TD>
<TD ALIGN=RIGHT>2000</TD>
<TD ALIGN=RIGHT>2000</TD>
   <TD ALIGN=CENTER>medium</TD></TR>
   <TD ALIGN=CENTER>medium</TD></TR>
Line 83: Line 83:
   <TD ALIGN=CENTER>Fugu</TD><TH ALIGN=CENTER>8.5X</TH>
   <TD ALIGN=CENTER>Fugu</TD><TH ALIGN=CENTER>8.5X</TH>
<TH ALIGN=CENTER>400509343</TH>
<TH ALIGN=CENTER>400509343</TH>
   <TH ALIGN=CENTER>N/A</TH><TD ALIGN=RIGHT>7.363%</TD>
   <TH ALIGN=CENTER>MAF net</TH><TD ALIGN=RIGHT>7.363%</TD>
<TD ALIGN=RIGHT>2000</TD>
<TD ALIGN=RIGHT>2000</TD>
   <TD ALIGN=CENTER>medium</TD></TR>
   <TD ALIGN=CENTER>medium</TD></TR>
Line 92: Line 92:
   <TD ALIGN=CENTER>X. tropicalis</TD><TH ALIGN=CENTER>7.65X</TH>
   <TD ALIGN=CENTER>X. tropicalis</TD><TH ALIGN=CENTER>7.65X</TH>
<TH ALIGN=CENTER>1564123</TH>
<TH ALIGN=CENTER>1564123</TH>
   <TH ALIGN=CENTER>N/A</TH><TD ALIGN=RIGHT>6.428%</TD>
   <TH ALIGN=CENTER>MAF net</TH><TD ALIGN=RIGHT>6.428%</TD>
<TD ALIGN=RIGHT>5000</TD>
<TD ALIGN=RIGHT>5000</TD>
   <TD ALIGN=CENTER>loose</TD></TR>
   <TD ALIGN=CENTER>loose</TD></TR>
Line 101: Line 101:
   <TD ALIGN=CENTER>Mouse</TD><TH ALIGN=CENTER>20X</TH>
   <TD ALIGN=CENTER>Mouse</TD><TH ALIGN=CENTER>20X</TH>
<TH ALIGN=CENTER>131738871</TH>
<TH ALIGN=CENTER>131738871</TH>
   <TH ALIGN=CENTER>N/A</TH><TD ALIGN=RIGHT>5.104%</TD>
   <TH ALIGN=CENTER>MAF net</TH><TD ALIGN=RIGHT>5.104%</TD>
<TD ALIGN=RIGHT>1000</TD>
<TD ALIGN=RIGHT>5000</TD>
   <TD ALIGN=CENTER>N/A</TD></TR>
   <TD ALIGN=CENTER>loose</TD></TR>
<TR><TH ALIGN=RIGHT>08</TH><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/data/index.shtml hg19]</TH>
<TR><TH ALIGN=RIGHT>08</TH><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/data/index.shtml hg19]</TH>
<TH ALIGN=RIGHT>93</TH>
<TH ALIGN=RIGHT>93</TH>
Line 110: Line 110:
   <TD ALIGN=CENTER>Human</TD><TH ALIGN=CENTER>20X</TH>
   <TD ALIGN=CENTER>Human</TD><TH ALIGN=CENTER>20X</TH>
<TH ALIGN=CENTER>146364022</TH>
<TH ALIGN=CENTER>146364022</TH>
   <TH ALIGN=CENTER>N/A</TH><TD ALIGN=RIGHT>6.151%</TD>
   <TH ALIGN=CENTER>MAF net</TH><TD ALIGN=RIGHT>6.151%</TD>
<TD ALIGN=RIGHT>1000</TD>
<TD ALIGN=RIGHT>5000</TD>
   <TD ALIGN=CENTER>N/A</TD></TR>
   <TD ALIGN=CENTER>loose</TD></TR>
</TABLE>
</TABLE>

Revision as of 21:55, 4 February 2011

see also

statistics collected from UCSC 2bit files

  • The external links from the UCSC database name go to the sequencing center information pages for this 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 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
  • % masked == masked either with WindowMasker or RepeatMasker plus TRF simple repeats
  • % of danRer7 matched (chainLink table) == featureBits danRer7 chain<Db>Link == alignment coverage

do not edit, automatically generated table

order
count		 ucsc
db name		 chrom
count		 total
size		 non-N
bases		 N base
count		 % masked common name coverage N50
chrom.sizes		 alignment type % of danRer7
matched
(chainLink table)		 chain
minScore		 chain
linearGap
01danRer7 1,133 1,412,464,8431,409,770,109 2,694,734% 52.06 Zebrafish30X 54093808 N/AN/A N/A N/A
02gasAcu1 23 463,354,448446,627,861 16,726,587% 2.58 Stickleback6X 20083130 MAF net10.270% 2000 medium
03oryLat2 7,189 869,000,216700,386,597 168,613,619% 33.09 Medaka10.6X 29908082 MAF net10.032% 2000 medium
04tetNig2 27 358,618,246302,314,788 56,303,458% 20.27 Tetraodon7.9X 13390619 MAF net6.273% 2000 medium
05fr2 2 400,525,790351,212,245 49,313,545% 19.01 Fugu8.5X 400509343 MAF net7.363% 2000 medium
06xenTro2 19,759 1,513,925,4921,359,400,017 154,525,475% 19.65 X. tropicalis7.65X 1564123 MAF net6.428% 5000 loose
07mm9 35 2,725,765,4812,620,345,972 105,419,509% 44.09 Mouse20X 131738871 MAF net5.104% 5000 loose
08hg19 93 3,137,161,2642,897,310,462 239,850,802% 50.63 Human20X 146364022 MAF net6.151% 5000 loose
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