Hg38 7-way Genome size statistics: Difference between revisions

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(correct alignment type)
 
Line 53: Line 53:
   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AACZ03 Chimp]</TD><TH ALIGN=CENTER>6X</TH>
   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AACZ03 Chimp]</TD><TH ALIGN=CENTER>6X</TH>
<TH ALIGN=CENTER>143986469</TH>
<TH ALIGN=CENTER>143986469</TH>
   <TH ALIGN=CENTER>Net</TH><TD ALIGN=RIGHT>93.112%</TD>
   <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>93.112%</TD>
<TD ALIGN=RIGHT>5000</TD>
<TD ALIGN=RIGHT>5000</TD>
   <TD ALIGN=CENTER>medium</TD></TR>
   <TD ALIGN=CENTER>medium</TD></TR>
Line 62: Line 62:
   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AEHK01 Rhesus]</TD><TH ALIGN=CENTER>50X</TH>
   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AEHK01 Rhesus]</TD><TH ALIGN=CENTER>50X</TH>
<TH ALIGN=CENTER>150158102</TH>
<TH ALIGN=CENTER>150158102</TH>
   <TH ALIGN=CENTER>Net</TH><TD ALIGN=RIGHT>79.729%</TD>
   <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>79.729%</TD>
<TD ALIGN=RIGHT>5000</TD>
<TD ALIGN=RIGHT>5000</TD>
   <TD ALIGN=CENTER>medium</TD></TR>
   <TD ALIGN=CENTER>medium</TD></TR>
Line 71: Line 71:
   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AAEX00 Dog]</TD><TH ALIGN=CENTER>7.6X</TH>
   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AAEX00 Dog]</TD><TH ALIGN=CENTER>7.6X</TH>
<TH ALIGN=CENTER>63241923</TH>
<TH ALIGN=CENTER>63241923</TH>
   <TH ALIGN=CENTER>Net</TH><TD ALIGN=RIGHT>49.978%</TD>
   <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>49.978%</TD>
<TD ALIGN=RIGHT>3000</TD>
<TD ALIGN=RIGHT>3000</TD>
   <TD ALIGN=CENTER>medium</TD></TR>
   <TD ALIGN=CENTER>medium</TD></TR>
Line 80: Line 80:
   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/bioproject/51977 Mouse]</TD><TH ALIGN=CENTER>20X</TH>
   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/bioproject/51977 Mouse]</TD><TH ALIGN=CENTER>20X</TH>
<TH ALIGN=CENTER>130694993</TH>
<TH ALIGN=CENTER>130694993</TH>
   <TH ALIGN=CENTER>Net</TH><TD ALIGN=RIGHT>31.629%</TD>
   <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>31.629%</TD>
<TD ALIGN=RIGHT>3000</TD>
<TD ALIGN=RIGHT>3000</TD>
   <TD ALIGN=CENTER>medium</TD></TR>
   <TD ALIGN=CENTER>medium</TD></TR>
Line 89: Line 89:
   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AABR06 Rat]</TD><TH ALIGN=CENTER>6X</TH>
   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AABR06 Rat]</TD><TH ALIGN=CENTER>6X</TH>
<TH ALIGN=CENTER>154597545</TH>
<TH ALIGN=CENTER>154597545</TH>
   <TH ALIGN=CENTER>Net</TH><TD ALIGN=RIGHT>30.788%</TD>
   <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>30.788%</TD>
<TD ALIGN=RIGHT>3000</TD>
<TD ALIGN=RIGHT>3000</TD>
   <TD ALIGN=CENTER>medium</TD></TR>
   <TD ALIGN=CENTER>medium</TD></TR>

Latest revision as of 18:19, 5 June 2014

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 hg38
matched
(chainLink table)		 chain
minScore		 chain
linearGap
01hg38 455 3,209,286,1053,049,315,783 159,970,322% 52.10 Human20X 145138636 N/AN/A 3000 medium
02panTro4 24,129 3,309,577,9222,902,338,967 407,238,955% 51.29 Chimp6X 143986469 SyntenicNet93.112% 5000 medium
03rheMac3 34,103 2,969,988,1802,639,145,830 330,842,350% 48.54 Rhesus50X 150158102 SyntenicNet79.729% 5000 medium
04canFam3 3,268 2,410,976,8752,392,715,236 18,261,639% 43.01 Dog7.6X 63241923 SyntenicNet49.978% 3000 medium
05mm10 66 2,730,871,7742,652,783,500 78,088,274% 45.18 Mouse20X 130694993 SyntenicNet31.629% 3000 medium
06rn5 2,739 2,909,698,9382,572,853,723 336,845,215% 42.81 Rat6X 154597545 SyntenicNet30.788% 3000 medium
07monDom5 11 3,605,631,7283,501,660,299 103,971,429% 55.95 Opossum6.8X 527952102 Net14.370% 5000 loose
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