PanTro3 Genome size statistics: Difference between revisions

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(initial contents does not include alignment type)
 
(all alignments are syntenic net)
Line 54: Line 54:
   <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>95.597%</TD>
   <TH ALIGN=CENTER>SynetnicNet</TH><TD ALIGN=RIGHT>95.597%</TD>
<TD ALIGN=RIGHT>1000</TD>
<TD ALIGN=RIGHT>5000</TD>
   <TD ALIGN=CENTER>N/A</TD></TR>
   <TD ALIGN=CENTER>medium</TD></TR>
<TR><TH ALIGN=RIGHT>03</TH><TH ALIGN=RIGHT>[http://genome.wustl.edu/genomes/view/pongo_abelii/ ponAbe2]</TH>
<TR><TH ALIGN=RIGHT>03</TH><TH ALIGN=RIGHT>[http://genome.wustl.edu/genomes/view/pongo_abelii/ ponAbe2]</TH>
<TH ALIGN=RIGHT>55</TH>
<TH ALIGN=RIGHT>55</TH>
Line 63: Line 63:
   <TD ALIGN=CENTER>Orangutan</TD><TH ALIGN=CENTER>6X</TH>
   <TD ALIGN=CENTER>Orangutan</TD><TH ALIGN=CENTER>6X</TH>
<TH ALIGN=CENTER>135191526</TH>
<TH ALIGN=CENTER>135191526</TH>
   <TH ALIGN=CENTER>N/A</TH><TD ALIGN=RIGHT>89.586%</TD>
   <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>89.586%</TD>
<TD ALIGN=RIGHT>5000</TD>
<TD ALIGN=RIGHT>5000</TD>
   <TD ALIGN=CENTER>medium</TD></TR>
   <TD ALIGN=CENTER>medium</TD></TR>
Line 72: Line 72:
   <TD ALIGN=CENTER>Rhesus</TD><TH ALIGN=CENTER>5.1X</TH>
   <TD ALIGN=CENTER>Rhesus</TD><TH ALIGN=CENTER>5.1X</TH>
<TH ALIGN=CENTER>153947521</TH>
<TH ALIGN=CENTER>153947521</TH>
   <TH ALIGN=CENTER>N/A</TH><TD ALIGN=RIGHT>81.342%</TD>
   <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>81.342%</TD>
<TD ALIGN=RIGHT>5000</TD>
<TD ALIGN=RIGHT>5000</TD>
   <TD ALIGN=CENTER>medium</TD></TR>
   <TD ALIGN=CENTER>medium</TD></TR>
Line 81: Line 81:
   <TD ALIGN=CENTER>Marmoset</TD><TH ALIGN=CENTER>6X</TH>
   <TD ALIGN=CENTER>Marmoset</TD><TH ALIGN=CENTER>6X</TH>
<TH ALIGN=CENTER>132174527</TH>
<TH ALIGN=CENTER>132174527</TH>
   <TH ALIGN=CENTER>N/A</TH><TD ALIGN=RIGHT>69.662%</TD>
   <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>69.662%</TD>
<TD ALIGN=RIGHT>5000</TD>
<TD ALIGN=RIGHT>5000</TD>
   <TD ALIGN=CENTER>medium</TD></TR>
   <TD ALIGN=CENTER>medium</TD></TR>
Line 90: Line 90:
   <TD ALIGN=CENTER>Horse</TD><TH ALIGN=CENTER>6.8X</TH>
   <TD ALIGN=CENTER>Horse</TD><TH ALIGN=CENTER>6.8X</TH>
<TH ALIGN=CENTER>91571448</TH>
<TH ALIGN=CENTER>91571448</TH>
   <TH ALIGN=CENTER>N/A</TH><TD ALIGN=RIGHT>56.504%</TD>
   <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>56.504%</TD>
<TD ALIGN=RIGHT>3000</TD>
<TD ALIGN=RIGHT>3000</TD>
   <TD ALIGN=CENTER>medium</TD></TR>
   <TD ALIGN=CENTER>medium</TD></TR>
Line 99: Line 99:
   <TD ALIGN=CENTER>Dog</TD><TH ALIGN=CENTER>7.6X</TH>
   <TD ALIGN=CENTER>Dog</TD><TH ALIGN=CENTER>7.6X</TH>
<TH ALIGN=CENTER>67211953</TH>
<TH ALIGN=CENTER>67211953</TH>
   <TH ALIGN=CENTER>N/A</TH><TD ALIGN=RIGHT>51.588%</TD>
   <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>51.588%</TD>
<TD ALIGN=RIGHT>3000</TD>
<TD ALIGN=RIGHT>3000</TD>
   <TD ALIGN=CENTER>medium</TD></TR>
   <TD ALIGN=CENTER>medium</TD></TR>
Line 108: Line 108:
   <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>32.044%</TD>
   <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>32.044%</TD>
<TD ALIGN=RIGHT>3000</TD>
<TD ALIGN=RIGHT>3000</TD>
   <TD ALIGN=CENTER>medium</TD></TR>
   <TD ALIGN=CENTER>medium</TD></TR>
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   <TD ALIGN=CENTER>Rat</TD><TH ALIGN=CENTER>20X</TH>
   <TD ALIGN=CENTER>Rat</TD><TH ALIGN=CENTER>20X</TH>
<TH ALIGN=CENTER>143002779</TH>
<TH ALIGN=CENTER>143002779</TH>
   <TH ALIGN=CENTER>N/A</TH><TD ALIGN=RIGHT>30.350%</TD>
   <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>30.350%</TD>
<TD ALIGN=RIGHT>3000</TD>
<TD ALIGN=RIGHT>3000</TD>
   <TD ALIGN=CENTER>medium</TD></TR>
   <TD ALIGN=CENTER>medium</TD></TR>
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   <TD ALIGN=CENTER>Opossum</TD><TH ALIGN=CENTER>6.8X</TH>
   <TD ALIGN=CENTER>Opossum</TD><TH ALIGN=CENTER>6.8X</TH>
<TH ALIGN=CENTER>527952102</TH>
<TH ALIGN=CENTER>527952102</TH>
   <TH ALIGN=CENTER>N/A</TH><TD ALIGN=RIGHT>13.743%</TD>
   <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>13.743%</TD>
<TD ALIGN=RIGHT>5000</TD>
<TD ALIGN=RIGHT>5000</TD>
   <TD ALIGN=CENTER>loose</TD></TR>
   <TD ALIGN=CENTER>loose</TD></TR>
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   <TD ALIGN=CENTER>Chicken</TD><TH ALIGN=CENTER>6.6X</TH>
   <TD ALIGN=CENTER>Chicken</TD><TH ALIGN=CENTER>6.6X</TH>
<TH ALIGN=CENTER>94230402</TH>
<TH ALIGN=CENTER>94230402</TH>
   <TH ALIGN=CENTER>N/A</TH><TD ALIGN=RIGHT>4.557%</TD>
   <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>4.557%</TD>
<TD ALIGN=RIGHT>5000</TD>
<TD ALIGN=RIGHT>5000</TD>
   <TD ALIGN=CENTER>loose</TD></TR>
   <TD ALIGN=CENTER>loose</TD></TR>
Line 144: Line 144:
   <TD ALIGN=CENTER>Zebrafish</TD><TH ALIGN=CENTER>30X</TH>
   <TD ALIGN=CENTER>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>2.558%</TD>
   <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>2.558%</TD>
<TD ALIGN=RIGHT>5000</TD>
<TD ALIGN=RIGHT>5000</TD>
   <TD ALIGN=CENTER>loose</TD></TR>
   <TD ALIGN=CENTER>loose</TD></TR>
</TABLE>
</TABLE>

Revision as of 18:16, 18 March 2011

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 hg19 matched (chainLink table) == featureBits hg19 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 panTro3
matched
(chainLink table)		 chain
minScore		 chain
linearGap
01panTro3 24,132 3,307,960,4322,900,529,764 407,430,668% 50.64 Chimp6X 143986469 N/AN/A 1000 N/A
02hg19 93 3,137,161,2642,897,310,462 239,850,802% 50.63 Human20X 146364022 SynetnicNet95.597% 5000 medium
03ponAbe2 55 3,446,771,3963,093,543,172 353,228,224% 50.89 Orangutan6X 135191526 SyntenicNet89.586% 5000 medium
04rheMac2 22 2,864,106,0712,646,668,809 217,437,262% 48.28 Rhesus5.1X 153947521 SyntenicNet81.342% 5000 medium
05calJac3 14,205 2,914,958,5442,752,505,800 162,452,744% 47.71 Marmoset6X 132174527 SyntenicNet69.662% 5000 medium
06equCab2 34 2,484,532,0622,428,790,173 55,741,889% 40.97 Horse6.8X 91571448 SyntenicNet56.504% 3000 medium
07canFam2 41 2,531,673,9532,384,996,543 146,677,410% 40.63 Dog7.6X 67211953 SyntenicNet51.588% 3000 medium
08mm9 35 2,725,765,4812,620,345,972 105,419,509% 44.09 Mouse20X 131738871 SyntenicNet32.044% 3000 medium
09rn4 45 2,834,127,2932,566,294,765 267,832,528% 44.29 Rat20X 143002779 SyntenicNet30.350% 3000 medium
10monDom5 11 3,605,631,7283,501,660,299 103,971,429% 55.95 Opossum6.8X 527952102 SyntenicNet13.743% 5000 loose
11galGal3 57 1,100,480,4411,042,583,135 57,897,306% 9.85 Chicken6.6X 94230402 SyntenicNet4.557% 5000 loose
12danRer7 1,133 1,412,464,8431,409,770,109 2,694,734% 52.06 Zebrafish30X 54093808 SyntenicNet2.558% 5000 loose
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