TarSyr2 17-way Genome size statistics: Difference between revisions
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<TD ALIGN=RIGHT>N/A</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>[http://www.ncbi.nlm.nih.gov/bioproject/ | <TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/bioproject/49285 02]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=panPan1 panPan1]</TH> | ||
<TH ALIGN=RIGHT>10,867</TH> | <TH ALIGN=RIGHT>10,867</TH> | ||
<TD ALIGN=RIGHT>2,869,190,071</TD><TD ALIGN=RIGHT>2,725,905,606</TD> | <TD ALIGN=RIGHT>2,869,190,071</TD><TD ALIGN=RIGHT>2,725,905,606</TD> | ||
| Line 74: | Line 56: | ||
<TD ALIGN=RIGHT>3000</TD> | <TD ALIGN=RIGHT>3000</TD> | ||
<TD ALIGN=CENTER>medium</TD></TR> | <TD ALIGN=CENTER>medium</TD></TR> | ||
<TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/bioproject/10627 03]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=panTro4 panTro4]</TH> | |||
<TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/bioproject/10627 | |||
<TH ALIGN=RIGHT>24,129</TH> | <TH ALIGN=RIGHT>24,129</TH> | ||
<TD ALIGN=RIGHT>3,309,577,922</TD><TD ALIGN=RIGHT>2,902,338,967</TD> | <TD ALIGN=RIGHT>3,309,577,922</TD><TD ALIGN=RIGHT>2,902,338,967</TD> | ||
| Line 92: | Line 65: | ||
<TD ALIGN=RIGHT>3000</TD> | <TD ALIGN=RIGHT>3000</TD> | ||
<TD ALIGN=CENTER>medium</TD></TR> | <TD ALIGN=CENTER>medium</TD></TR> | ||
<TR><TH ALIGN=RIGHT>[http://genome.wustl.edu/genomes/view/pongo_abelii/ 04]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=ponAbe2 ponAbe2]</TH> | |||
<TR><TH ALIGN=RIGHT>[http://genome.wustl.edu/genomes/view/pongo_abelii/ | |||
<TH ALIGN=RIGHT>55</TH> | <TH ALIGN=RIGHT>55</TH> | ||
<TD ALIGN=RIGHT>3,446,771,396</TD><TD ALIGN=RIGHT>3,093,543,172</TD> | <TD ALIGN=RIGHT>3,446,771,396</TD><TD ALIGN=RIGHT>3,093,543,172</TD> | ||
| Line 110: | Line 74: | ||
<TD ALIGN=RIGHT>3000</TD> | <TD ALIGN=RIGHT>3000</TD> | ||
<TD ALIGN=CENTER>medium</TD></TR> | <TD ALIGN=CENTER>medium</TD></TR> | ||
<TR><TH ALIGN=RIGHT>[ | <TR><TH ALIGN=RIGHT>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Gorilla_gorilla/gorGor3.1/ 05]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=gorGor3 gorGor3]</TH> | ||
<TH ALIGN=RIGHT> | <TH ALIGN=RIGHT>46,823</TH> | ||
<TD ALIGN=RIGHT>3, | <TD ALIGN=RIGHT>3,029,553,646</TD><TD ALIGN=RIGHT>2,822,760,080</TD> | ||
<TD ALIGN=RIGHT> | <TD ALIGN=RIGHT>206,793,566</TD><TD ALIGN=RIGHT>% 48.80</TD> | ||
<TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val= | <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=CABD02 Gorilla]</TD><TH ALIGN=CENTER>2.1X</TH> | ||
<TH ALIGN=CENTER> | <TH ALIGN=CENTER>145327772</TH> | ||
< | <TD ALIGN=CENTER>RecipBest</TD><TD ALIGN=RIGHT>50.262%</TD> | ||
<TD ALIGN=RIGHT>3000</TD> | <TD ALIGN=RIGHT>3000</TD> | ||
<TD ALIGN=CENTER>medium</TD></TR> | <TD ALIGN=CENTER>medium</TD></TR> | ||
<TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/ | <TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/assembly/GCA_000146795.3/ 06]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=nomLeu3 nomLeu3]</TH> | ||
<TH ALIGN=RIGHT> | <TH ALIGN=RIGHT>17,492</TH> | ||
<TD ALIGN=RIGHT> | <TD ALIGN=RIGHT>2,962,077,449</TD><TD ALIGN=RIGHT>2,756,609,047</TD> | ||
<TD ALIGN=RIGHT> | <TD ALIGN=RIGHT>205,468,402</TD><TD ALIGN=RIGHT>% 51.14</TD> | ||
<TD ALIGN=CENTER>[ | <TD ALIGN=CENTER>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Nomascus_leucogenys/Nleu_3.0/ Gibbon]</TD><TH ALIGN=CENTER>5.6X</TH> | ||
<TH ALIGN=CENTER> | <TH ALIGN=CENTER>117381234</TH> | ||
<TH ALIGN=CENTER> | <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>50.545%</TD> | ||
<TD ALIGN=RIGHT>3000</TD> | <TD ALIGN=RIGHT>3000</TD> | ||
<TD ALIGN=CENTER>medium</TD></TR> | <TD ALIGN=CENTER>medium</TD></TR> | ||
<TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/assembly/GCA_000364345.1/ 07]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=macFas5 macFas5]</TH> | |||
<TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/assembly/GCA_000364345.1/ | |||
<TH ALIGN=RIGHT>7,601</TH> | <TH ALIGN=RIGHT>7,601</TH> | ||
<TD ALIGN=RIGHT>2,946,843,737</TD><TD ALIGN=RIGHT>2,803,866,385</TD> | <TD ALIGN=RIGHT>2,946,843,737</TD><TD ALIGN=RIGHT>2,803,866,385</TD> | ||
| Line 146: | Line 101: | ||
<TD ALIGN=RIGHT>3000</TD> | <TD ALIGN=RIGHT>3000</TD> | ||
<TD ALIGN=CENTER>medium</TD></TR> | <TD ALIGN=CENTER>medium</TD></TR> | ||
<TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/genome/assembly/310688/ | <TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/bioproject/54005 08]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=papAnu2 papAnu2]</TH> | ||
<TH ALIGN=RIGHT>63,250</TH> | |||
<TD ALIGN=RIGHT>2,948,380,710</TD><TD ALIGN=RIGHT>2,893,250,291</TD> | |||
<TD ALIGN=RIGHT>55,130,419</TD><TD ALIGN=RIGHT>% 38.95</TD> | |||
<TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AHZZ01 Baboon]</TD><TH ALIGN=CENTER>85X</TH> | |||
<TH ALIGN=CENTER>139646187</TH> | |||
<TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>51.652%</TD> | |||
<TD ALIGN=RIGHT>3000</TD> | |||
<TD ALIGN=CENTER>medium</TD></TR> | |||
<TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/genome/assembly/310688/ 09]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=rheMac3 rheMac3]</TH> | |||
<TH ALIGN=RIGHT>34,103</TH> | <TH ALIGN=RIGHT>34,103</TH> | ||
<TD ALIGN=RIGHT>2,969,988,180</TD><TD ALIGN=RIGHT>2,639,145,830</TD> | <TD ALIGN=RIGHT>2,969,988,180</TD><TD ALIGN=RIGHT>2,639,145,830</TD> | ||
| Line 155: | Line 119: | ||
<TD ALIGN=RIGHT>3000</TD> | <TD ALIGN=RIGHT>3000</TD> | ||
<TD ALIGN=CENTER>medium</TD></TR> | <TD ALIGN=CENTER>medium</TD></TR> | ||
<TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/bioproject/ | <TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/bioproject/PRJNA168621 10]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=chlSab2 chlSab2]</TH> | ||
<TH ALIGN=RIGHT> | <TH ALIGN=RIGHT>2,004</TH> | ||
<TD ALIGN=RIGHT>2, | <TD ALIGN=RIGHT>2,789,656,328</TD><TD ALIGN=RIGHT>2,752,000,999</TD> | ||
<TD ALIGN=RIGHT> | <TD ALIGN=RIGHT>37,655,329</TD><TD ALIGN=RIGHT>% 48.77</TD> | ||
<TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val= | <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AQIB01 Green monkey]</TD><TH ALIGN=CENTER>95X</TH> | ||
<TH ALIGN=CENTER> | <TH ALIGN=CENTER>101219884</TH> | ||
<TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>51. | <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>51.691%</TD> | ||
<TD ALIGN=RIGHT>3000</TD> | |||
<TD ALIGN=CENTER>medium</TD></TR> | |||
<TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/assembly/GCA_000001405.15/ 11]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=hg38 hg38]</TH> | |||
<TH ALIGN=RIGHT>455</TH> | |||
<TD ALIGN=RIGHT>3,209,286,105</TD><TD ALIGN=RIGHT>3,049,315,783</TD> | |||
<TD ALIGN=RIGHT>159,970,322</TD><TD ALIGN=RIGHT>% 52.10</TD> | |||
<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>145138636</TH> | |||
<TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>52.305%</TD> | |||
<TD ALIGN=RIGHT>3000</TD> | |||
<TD ALIGN=CENTER>medium</TD></TR> | |||
<TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/bioproject/PRJNA266995 12]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=rhiRox1 rhiRox1]</TH> | |||
<TH ALIGN=RIGHT>135,512</TH> | |||
<TD ALIGN=RIGHT>2,899,552,139</TD><TD ALIGN=RIGHT>2,856,044,136</TD> | |||
<TD ALIGN=RIGHT>43,508,003</TD><TD ALIGN=RIGHT>% 51.07</TD> | |||
<TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=JABR01 Golden snub-nosed monkey]</TD><TH ALIGN=CENTER>53.7X</TH> | |||
<TH ALIGN=CENTER>137426304</TH> | |||
<TH ALIGN=CENTER>RecipBest</TH><TD ALIGN=RIGHT>51.539%</TD> | |||
<TD ALIGN=RIGHT>3000</TD> | |||
<TD ALIGN=CENTER>medium</TD></TR> | |||
<TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/bioproject/PRJNA241312 13]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=nasLar1 nasLar1]</TH> | |||
<TH ALIGN=RIGHT>319,550</TH> | |||
<TD ALIGN=RIGHT>3,011,982,740</TD><TD ALIGN=RIGHT>2,397,109,760</TD> | |||
<TD ALIGN=RIGHT>614,872,980</TD><TD ALIGN=RIGHT>% 46.33</TD> | |||
<TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=JMHX01 Proboscis monkey]</TD><TH ALIGN=CENTER>290X</TH> | |||
<TH ALIGN=CENTER>137426304</TH> | |||
<TH ALIGN=CENTER>RecipBest</TH><TD ALIGN=RIGHT>47.164%</TD> | |||
<TD ALIGN=RIGHT>3000</TD> | <TD ALIGN=RIGHT>3000</TD> | ||
<TD ALIGN=CENTER>medium</TD></TR> | <TD ALIGN=CENTER>medium</TD></TR> | ||
<TR><TH ALIGN=RIGHT>[http:// | <TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/bioproject/67945 14]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=saiBol1 saiBol1]</TH> | ||
<TH ALIGN=RIGHT> | <TH ALIGN=RIGHT>2,685</TH> | ||
<TD ALIGN=RIGHT>2, | <TD ALIGN=RIGHT>2,608,572,064</TD><TD ALIGN=RIGHT>2,477,131,095</TD> | ||
<TD ALIGN=RIGHT> | <TD ALIGN=RIGHT>131,440,969</TD><TD ALIGN=RIGHT>% 46.69</TD> | ||
<TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val= | <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AGCE01 Squirrel monkey]</TD><TH ALIGN=CENTER>80X</TH> | ||
<TH ALIGN=CENTER> | <TH ALIGN=CENTER>18744880</TH> | ||
<TH ALIGN=CENTER> | <TH ALIGN=CENTER>RecipBest</TH><TD ALIGN=RIGHT>48.208%</TD> | ||
<TD ALIGN=RIGHT>3000</TD> | <TD ALIGN=RIGHT>3000</TD> | ||
<TD ALIGN=CENTER>medium</TD></TR> | <TD ALIGN=CENTER>medium</TD></TR> | ||
<TR><TH ALIGN=RIGHT>[http://www.broadinstitute.org/ftp/pub/assemblies/mammals/mouseLemur/MicMur1.0/ | <TR><TH ALIGN=RIGHT>[http://www.broadinstitute.org/ftp/pub/assemblies/mammals/mouseLemur/MicMur1.0/ 15]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=micMur1 micMur1]</TH> | ||
<TH ALIGN=RIGHT>185,042</TH> | <TH ALIGN=RIGHT>185,042</TH> | ||
<TD ALIGN=RIGHT>2,902,270,736</TD><TD ALIGN=RIGHT>1,852,394,361</TD> | <TD ALIGN=RIGHT>2,902,270,736</TD><TD ALIGN=RIGHT>1,852,394,361</TD> | ||
| Line 180: | Line 171: | ||
<TH ALIGN=CENTER>140884</TH> | <TH ALIGN=CENTER>140884</TH> | ||
<TD ALIGN=CENTER>RecipBest</TD><TD ALIGN=RIGHT>38.087%</TD> | <TD ALIGN=CENTER>RecipBest</TD><TD ALIGN=RIGHT>38.087%</TD> | ||
<TD ALIGN=RIGHT>3000</TD> | |||
<TD ALIGN=CENTER>medium</TD></TR> | |||
<TR><TH ALIGN=RIGHT>[http://genome.wustl.edu/genomes/view/callithrix_jacchus/ 16]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=calJac3 calJac3]</TH> | |||
<TH ALIGN=RIGHT>14,205</TH> | |||
<TD ALIGN=RIGHT>2,914,958,544</TD><TD ALIGN=RIGHT>2,752,505,800</TD> | |||
<TD ALIGN=RIGHT>162,452,744</TD><TD ALIGN=RIGHT>% 47.71</TD> | |||
<TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ACFV00 Marmoset]</TD><TH ALIGN=CENTER>6X</TH> | |||
<TH ALIGN=CENTER>132174527</TH> | |||
<TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>48.629%</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 18:43, 26 February 2015
see also
- Tarsier 17-way TarSyr2 17-way conservation alignment
- Tarsier 17-way TarSyr2 17-way conservation lastz parameters
- all other UCSC Multiple Alignments
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 tarSyr2 matched (chainLink table) |
chain minScore |
chain linearGap |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 01 | tarSyr2 | 337,189 | 3,453,864,774 | 3,405,755,564 | 48,109,210 | % 47.85 | Tarsier | 48X | 401181 | N/A | N/A | N/A | N/A |
| 02 | panPan1 | 10,867 | 2,869,190,071 | 2,725,905,606 | 143,284,465 | % 36.53 | Bonobo | 26X | 10124892 | RecipBest | 52.289% | 3000 | medium |
| 03 | panTro4 | 24,129 | 3,309,577,922 | 2,902,338,967 | 407,238,955 | % 51.29 | Chimp | 6X | 143986469 | SyntenicNet | 51.284% | 3000 | medium |
| 04 | ponAbe2 | 55 | 3,446,771,396 | 3,093,543,172 | 353,228,224 | % 50.89 | Orangutan | 6X | 135191526 | SyntenicNet | 51.302% | 3000 | medium |
| 05 | gorGor3 | 46,823 | 3,029,553,646 | 2,822,760,080 | 206,793,566 | % 48.80 | Gorilla | 2.1X | 145327772 | RecipBest | 50.262% | 3000 | medium |
| 06 | nomLeu3 | 17,492 | 2,962,077,449 | 2,756,609,047 | 205,468,402 | % 51.14 | Gibbon | 5.6X | 117381234 | SyntenicNet | 50.545% | 3000 | medium |
| 07 | macFas5 | 7,601 | 2,946,843,737 | 2,803,866,385 | 142,977,352 | % 50.11 | Crab-eating macaque | 68X | 152835861 | SyntenicNet | 51.814% | 3000 | medium |
| 08 | papAnu2 | 63,250 | 2,948,380,710 | 2,893,250,291 | 55,130,419 | % 38.95 | Baboon | 85X | 139646187 | SyntenicNet | 51.652% | 3000 | medium |
| 09 | rheMac3 | 34,103 | 2,969,988,180 | 2,639,145,830 | 330,842,350 | % 48.54 | Rhesus | 50X | 150158102 | SyntenicNet | 50.710% | 3000 | medium |
| 10 | chlSab2 | 2,004 | 2,789,656,328 | 2,752,000,999 | 37,655,329 | % 48.77 | Green monkey | 95X | 101219884 | SyntenicNet | 51.691% | 3000 | medium |
| 11 | hg38 | 455 | 3,209,286,105 | 3,049,315,783 | 159,970,322 | % 52.10 | Human | 20X | 145138636 | SyntenicNet | 52.305% | 3000 | medium |
| 12 | rhiRox1 | 135,512 | 2,899,552,139 | 2,856,044,136 | 43,508,003 | % 51.07 | Golden snub-nosed monkey | 53.7X | 137426304 | RecipBest | 51.539% | 3000 | medium |
| 13 | nasLar1 | 319,550 | 3,011,982,740 | 2,397,109,760 | 614,872,980 | % 46.33 | Proboscis monkey | 290X | 137426304 | RecipBest | 47.164% | 3000 | medium |
| 14 | saiBol1 | 2,685 | 2,608,572,064 | 2,477,131,095 | 131,440,969 | % 46.69 | Squirrel monkey | 80X | 18744880 | RecipBest | 48.208% | 3000 | medium |
| 15 | micMur1 | 185,042 | 2,902,270,736 | 1,852,394,361 | 1,049,876,375 | % 37.31 | Mouse lemur | 2X | 140884 | RecipBest | 38.087% | 3000 | medium |
| 16 | calJac3 | 14,205 | 2,914,958,544 | 2,752,505,800 | 162,452,744 | % 47.71 | Marmoset | 6X | 132174527 | SyntenicNet | 48.629% | 3000 | medium |
| 17 | otoGar3 | 7,793 | 2,519,724,550 | 2,359,530,453 | 160,194,097 | % 39.51 | Bushbaby | 137X | 13852661 | RecipBest | 44.814% | 3000 | medium |
