GeoFor1 Genome size statistics: Difference between revisions

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   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ABQF00 Zebra finch]</TD><TH ALIGN=CENTER>6X</TH>
   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ABQF00 Zebra finch]</TD><TH ALIGN=CENTER>6X</TH>
<TH ALIGN=CENTER>73657157</TH>
<TH ALIGN=CENTER>73657157</TH>
   <TH ALIGN=CENTER>Net</TH><TD ALIGN=RIGHT>92.532%</TD>
   <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>92.532%</TD>
<TD ALIGN=RIGHT>1000</TD>
<TD ALIGN=RIGHT>1000</TD>
   <TD ALIGN=CENTER>loose</TD></TR>
   <TD ALIGN=CENTER>loose</TD></TR>
<TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/genome/111 03]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=galGal4 galGal4]</TH>
<TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/genome/10765 03]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=melUnd1 melUnd1]</TH>
<TH ALIGN=RIGHT>25,212</TH>
  <TD ALIGN=RIGHT>1,117,373,619</TD><TD ALIGN=RIGHT>1,086,614,815</TD>
  <TD ALIGN=RIGHT>30,758,804</TD><TD ALIGN=RIGHT>%&nbsp;19.62</TD>
  <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AGAI01 Budgerigar]</TD><TH ALIGN=CENTER>7X</TH>
<TH ALIGN=CENTER>10614383</TH>
  <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>80.650%</TD>
<TD ALIGN=RIGHT>1000</TD>
  <TD ALIGN=CENTER>loose</TD></TR>
<TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/genome/111 04]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=galGal4 galGal4]</TH>
<TH ALIGN=RIGHT>15,932</TH>
<TH ALIGN=RIGHT>15,932</TH>
   <TD ALIGN=RIGHT>1,046,932,099</TD><TD ALIGN=RIGHT>1,032,854,810</TD>
   <TD ALIGN=RIGHT>1,046,932,099</TD><TD ALIGN=RIGHT>1,032,854,810</TD>
Line 62: Line 71:
   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AADN00 Chicken]</TD><TH ALIGN=CENTER>12X</TH>
   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AADN00 Chicken]</TD><TH ALIGN=CENTER>12X</TH>
<TH ALIGN=CENTER>90216835</TH>
<TH ALIGN=CENTER>90216835</TH>
   <TH ALIGN=CENTER>Net</TH><TD ALIGN=RIGHT>70.718%</TD>
   <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>70.718%</TD>
<TD ALIGN=RIGHT>1000</TD>
<TD ALIGN=RIGHT>1000</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/ 04]</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/ 05]</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 71: Line 80:
   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ADDD00 Turkey]</TD><TH ALIGN=CENTER>5X</TH>
   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ADDD00 Turkey]</TD><TH ALIGN=CENTER>5X</TH>
<TH ALIGN=CENTER>74864452</TH>
<TH ALIGN=CENTER>74864452</TH>
   <TH ALIGN=CENTER>Net</TH><TD ALIGN=RIGHT>67.079%</TD>
   <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>67.079%</TD>
<TD ALIGN=RIGHT>1000</TD>
  <TD ALIGN=CENTER>loose</TD></TR>
<TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/genome/10765 05]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=melUnd1 melUnd1]</TH>
<TH ALIGN=RIGHT>25,212</TH>
  <TD ALIGN=RIGHT>1,117,373,619</TD><TD ALIGN=RIGHT>1,086,614,815</TD>
  <TD ALIGN=RIGHT>30,758,804</TD><TD ALIGN=RIGHT>%&nbsp;19.62</TD>
  <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AGAI01 Budgerigar]</TD><TH ALIGN=CENTER>7X</TH>
<TH ALIGN=CENTER>10614383</TH>
  <TH ALIGN=CENTER>Net</TH><TD ALIGN=RIGHT>80.650%</TD>
<TD ALIGN=RIGHT>1000</TD>
<TD ALIGN=RIGHT>1000</TD>
   <TD ALIGN=CENTER>loose</TD></TR>
   <TD ALIGN=CENTER>loose</TD></TR>
Line 89: Line 89:
   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/index.shtml Human]</TD><TH ALIGN=CENTER>20X</TH>
   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/index.shtml Human]</TD><TH ALIGN=CENTER>20X</TH>
<TH ALIGN=CENTER>146364022</TH>
<TH ALIGN=CENTER>146364022</TH>
   <TH ALIGN=CENTER>Net</TH><TD ALIGN=RIGHT>8.504%</TD>
   <TH ALIGN=CENTER>RecipBest</TH><TD ALIGN=RIGHT>8.504%</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>[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>7.709%</TD>
   <TH ALIGN=CENTER>RecipBest</TH><TD ALIGN=RIGHT>7.709%</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 23:26, 2 August 2012

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 geoFor1
matched
(chainLink table)
chain
minScore
chain
linearGap
01geoFor1 27,239 1,065,292,1811,041,286,029 24,006,152% 19.99 Medium ground finch115X 5255844 N/AN/A N/A N/A
02taeGut1 70 1,233,186,3411,222,864,691 10,321,650% 20.42 Zebra finch6X 73657157 SyntenicNet92.532% 1000 loose
03melUnd1 25,212 1,117,373,6191,086,614,815 30,758,804% 19.62 Budgerigar7X 10614383 SyntenicNet80.650% 1000 loose
04galGal4 15,932 1,046,932,0991,032,854,810 14,077,289% 20.41 Chicken12X 90216835 SyntenicNet70.718% 1000 loose
05melGal1 5,891 1,061,817,101935,922,386 125,894,715% 6.60 Turkey5X 74864452 SyntenicNet67.079% 1000 loose
06hg19 93 3,137,161,2642,897,310,462 239,850,802% 50.63 Human20X 146364022 RecipBest8.504% 5000 loose
07mm10 66 2,730,871,7742,652,783,500 78,088,274% 45.18 Mouse20X 130694993 RecipBest7.709% 5000 loose