Fr3 Genome size statistics: Difference between revisions
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(updated to 8-way) |
(Updated hgwdev/genome-test links to .gi, all links validated) |
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<TH>chain<BR>linearGap</TH> | <TH>chain<BR>linearGap</TH> | ||
<TR> | <TR> | ||
<TR><TH ALIGN=RIGHT>[http://www.fugu-sg.org/ 01]</TH><TH ALIGN=RIGHT>[http://genome-test. | <TR><TH ALIGN=RIGHT>[http://www.fugu-sg.org/ 01]</TH><TH ALIGN=RIGHT>[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=fr3 fr3]</TH> | ||
<TH ALIGN=RIGHT>6,835</TH> | <TH ALIGN=RIGHT>6,835</TH> | ||
<TD ALIGN=RIGHT>391,484,715</TD><TD ALIGN=RIGHT>350,961,831</TD> | <TD ALIGN=RIGHT>391,484,715</TD><TD ALIGN=RIGHT>350,961,831</TD> | ||
| Line 47: | Line 47: | ||
<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.genoscope.cns.fr/spip/Tetraodon-nigroviridis-a-fish-with.html 02]</TH><TH ALIGN=RIGHT>[http://genome-test. | <TR><TH ALIGN=RIGHT>[http://www.genoscope.cns.fr/spip/Tetraodon-nigroviridis-a-fish-with.html 02]</TH><TH ALIGN=RIGHT>[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=tetNig2 tetNig2]</TH> | ||
<TH ALIGN=RIGHT>27</TH> | <TH ALIGN=RIGHT>27</TH> | ||
<TD ALIGN=RIGHT>358,618,246</TD><TD ALIGN=RIGHT>302,314,788</TD> | <TD ALIGN=RIGHT>358,618,246</TD><TD ALIGN=RIGHT>302,314,788</TD> | ||
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<TD ALIGN=RIGHT>2000</TD> | <TD ALIGN=RIGHT>2000</TD> | ||
<TD ALIGN=CENTER>medium</TD></TR> | <TD ALIGN=CENTER>medium</TD></TR> | ||
<TR><TH ALIGN=RIGHT>[ftp://ftp.broadinstitute.org/pub/assemblies/fish/tilapia/Orenil1/ 03]</TH><TH ALIGN=RIGHT>[http://genome-test. | <TR><TH ALIGN=RIGHT>[ftp://ftp.broadinstitute.org/pub/assemblies/fish/tilapia/Orenil1/ 03]</TH><TH ALIGN=RIGHT>[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=oreNil1 oreNil1]</TH> | ||
<TH ALIGN=RIGHT>5,901</TH> | <TH ALIGN=RIGHT>5,901</TH> | ||
<TD ALIGN=RIGHT>927,742,539</TD><TD ALIGN=RIGHT>816,084,674</TD> | <TD ALIGN=RIGHT>927,742,539</TD><TD ALIGN=RIGHT>816,084,674</TD> | ||
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<TD ALIGN=RIGHT>2000</TD> | <TD ALIGN=RIGHT>2000</TD> | ||
<TD ALIGN=CENTER>medium</TD></TR> | <TD ALIGN=CENTER>medium</TD></TR> | ||
<TR><TH ALIGN=RIGHT>[ftp://ftp.broadinstitute.org/pub/assemblies/fish/stickleback/gasAcu1/ 04]</TH><TH ALIGN=RIGHT>[http://genome-test. | <TR><TH ALIGN=RIGHT>[ftp://ftp.broadinstitute.org/pub/assemblies/fish/stickleback/gasAcu1/ 04]</TH><TH ALIGN=RIGHT>[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=gasAcu1 gasAcu1]</TH> | ||
<TH ALIGN=RIGHT>23</TH> | <TH ALIGN=RIGHT>23</TH> | ||
<TD ALIGN=RIGHT>463,354,448</TD><TD ALIGN=RIGHT>446,627,861</TD> | <TD ALIGN=RIGHT>463,354,448</TD><TD ALIGN=RIGHT>446,627,861</TD> | ||
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<TD ALIGN=RIGHT>2000</TD> | <TD ALIGN=RIGHT>2000</TD> | ||
<TD ALIGN=CENTER>medium</TD></TR> | <TD ALIGN=CENTER>medium</TD></TR> | ||
<TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/genome/2661 05]</TH><TH ALIGN=RIGHT>[http://genome-test. | <TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/genome/2661 05]</TH><TH ALIGN=RIGHT>[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=gadMor1 gadMor1]</TH> | ||
<TH ALIGN=RIGHT>427,428</TH> | <TH ALIGN=RIGHT>427,428</TH> | ||
<TD ALIGN=RIGHT>824,327,835</TD><TD ALIGN=RIGHT>608,038,555</TD> | <TD ALIGN=RIGHT>824,327,835</TD><TD ALIGN=RIGHT>608,038,555</TD> | ||
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<TD ALIGN=RIGHT>2000</TD> | <TD ALIGN=RIGHT>2000</TD> | ||
<TD ALIGN=CENTER>medium</TD></TR> | <TD ALIGN=CENTER>medium</TD></TR> | ||
<TR><TH ALIGN=RIGHT>[http://dolphin.lab.nig.ac.jp/medaka/index.php 06]</TH><TH ALIGN=RIGHT>[http://genome-test. | <TR><TH ALIGN=RIGHT>[http://dolphin.lab.nig.ac.jp/medaka/index.php 06]</TH><TH ALIGN=RIGHT>[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=oryLat2 oryLat2]</TH> | ||
<TH ALIGN=RIGHT>7,189</TH> | <TH ALIGN=RIGHT>7,189</TH> | ||
<TD ALIGN=RIGHT>869,000,216</TD><TD ALIGN=RIGHT>700,386,597</TD> | <TD ALIGN=RIGHT>869,000,216</TD><TD ALIGN=RIGHT>700,386,597</TD> | ||
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<TD ALIGN=RIGHT>2000</TD> | <TD ALIGN=RIGHT>2000</TD> | ||
<TD ALIGN=CENTER>medium</TD></TR> | <TD ALIGN=CENTER>medium</TD></TR> | ||
<TR><TH ALIGN=RIGHT>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_other/Danio_rerio/Zv9/ 07]</TH><TH ALIGN=RIGHT>[http://genome-test. | <TR><TH ALIGN=RIGHT>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_other/Danio_rerio/Zv9/ 07]</TH><TH ALIGN=RIGHT>[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=danRer7 danRer7]</TH> | ||
<TH ALIGN=RIGHT>1,133</TH> | <TH ALIGN=RIGHT>1,133</TH> | ||
<TD ALIGN=RIGHT>1,412,464,843</TD><TD ALIGN=RIGHT>1,409,770,109</TD> | <TD ALIGN=RIGHT>1,412,464,843</TD><TD ALIGN=RIGHT>1,409,770,109</TD> | ||
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<TD ALIGN=RIGHT>2000</TD> | <TD ALIGN=RIGHT>2000</TD> | ||
<TD ALIGN=CENTER>medium</TD></TR> | <TD ALIGN=CENTER>medium</TD></TR> | ||
<TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/bioproject/56111 08]</TH><TH ALIGN=RIGHT>[http://genome-test. | <TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/bioproject/56111 08]</TH><TH ALIGN=RIGHT>[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=latCha1 latCha1]</TH> | ||
<TH ALIGN=RIGHT>22,819</TH> | <TH ALIGN=RIGHT>22,819</TH> | ||
<TD ALIGN=RIGHT>2,860,591,921</TD><TD ALIGN=RIGHT>2,183,592,768</TD> | <TD ALIGN=RIGHT>2,860,591,921</TD><TD ALIGN=RIGHT>2,183,592,768</TD> | ||
Latest revision as of 21:37, 30 August 2018
see also
- Fugu 8-way Fr3 conservation alignment
- Fugu 8-way Fr3 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 fr3 matched (chainLink table) |
chain minScore |
chain linearGap |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 01 | fr3 | 6,835 | 391,484,715 | 350,961,831 | 40,522,884 | % 19.01 | Fugu | 8.5X | 11516971 | N/A | N/A | N/A | N/A |
| 02 | tetNig2 | 27 | 358,618,246 | 302,314,788 | 56,303,458 | % 20.27 | Tetraodon | 7.9X | 13390619 | Net | 70.912% | 2000 | medium |
| 03 | oreNil1 | 5,901 | 927,742,539 | 816,084,674 | 111,657,865 | % 25.51 | Nile tilapia | 269X | 2802423 | Net | 57.240% | 2000 | medium |
| 04 | gasAcu1 | 23 | 463,354,448 | 446,627,861 | 16,726,587 | % 2.58 | Stickleback | 6X | 20083130 | Net | 55.527% | 2000 | medium |
| 05 | gadMor1 | 427,428 | 824,327,835 | 608,038,555 | 216,289,280 | % 31.25 | Atlantic cod | 40X | 393166 | Net | 30.327% | 2000 | medium |
| 06 | oryLat2 | 7,189 | 869,000,216 | 700,386,597 | 168,613,619 | % 33.09 | Medaka | 10.6X | 29908082 | Net | 43.863% | 2000 | medium |
| 07 | danRer7 | 1,133 | 1,412,464,843 | 1,409,770,109 | 2,694,734 | % 52.06 | Zebrafish | 30X | 54093808 | Net | 22.823% | 2000 | medium |
| 08 | latCha1 | 22,819 | 2,860,591,921 | 2,183,592,768 | 676,999,153 | % 45.68 | Coelacanth | 77.5X | 924513 | Net | 13.735% | 2000 | medium |
