Hg19 conservation alignment: Difference between revisions
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This table is automatically generated off-line from the UCSC databases. Please do | This table is automatically generated off-line from the UCSC databases. Please do | ||
not edit it. | not edit it. | ||
<TABLE BORDER=1> | <TABLE BORDER=1> | ||
<TR> | <TR> | ||
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<TD>Broad Institute choHof1</TD> | <TD>Broad Institute choHof1</TD> | ||
<TD ALIGN=RIGHT>2008-10-16</TD> | <TD ALIGN=RIGHT>2008-10-16</TD> | ||
<TD ALIGN=RIGHT>N/A</TD><TD>2009-05-26</TD><TD ALIGN=RIGHT> | <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-26</TD><TD ALIGN=RIGHT>34.376%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>29</TH><TH>dipOrd1</TH><TD>Dipodomys<BR>ordii</TD><TD>Kangaroo rat</TD> | <TH>29</TH><TH>dipOrd1</TH><TD>Dipodomys<BR>ordii</TD><TD>Kangaroo rat</TD> | ||
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<TD>Broad Institute dasNov2 (NCBI project 12594, AAGV020000000)</TD> | <TD>Broad Institute dasNov2 (NCBI project 12594, AAGV020000000)</TD> | ||
<TD ALIGN=RIGHT>2008-10-07</TD> | <TD ALIGN=RIGHT>2008-10-07</TD> | ||
<TD ALIGN=RIGHT>N/A</TD><TD> | <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-27</TD><TD ALIGN=RIGHT>N/A</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>36</TH><TH>monDom5</TH><TD>Monodelphis<BR>domestica</TD><TD>Opossum</TD> | <TH>36</TH><TH>monDom5</TH><TD>Monodelphis<BR>domestica</TD><TD>Opossum</TD> | ||
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<TD>WUSTL version 5.0.1</TD> | <TD>WUSTL version 5.0.1</TD> | ||
<TD ALIGN=RIGHT>2007-07-20</TD> | <TD ALIGN=RIGHT>2007-07-20</TD> | ||
<TD ALIGN=RIGHT>N/A</TD><TD> | <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-27</TD><TD ALIGN=RIGHT>7.627%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>38</TH><TH>galGal3</TH><TD>Gallus<BR>gallus</TD><TD>Chicken</TD> | <TH>38</TH><TH>galGal3</TH><TD>Gallus<BR>gallus</TD><TD>Chicken</TD> | ||
| Line 314: | Line 315: | ||
<TD>JGI v4.1</TD> | <TD>JGI v4.1</TD> | ||
<TD ALIGN=RIGHT>2006-04-17</TD> | <TD ALIGN=RIGHT>2006-04-17</TD> | ||
<TD ALIGN=RIGHT>2007-02-20</TD><TD> | <TD ALIGN=RIGHT>2007-02-20</TD><TD>2009-05-27</TD><TD ALIGN=RIGHT>3.176%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>42</TH><TH>danRer5</TH><TD>Danio<BR>rerio</TD><TD>Zebrafish</TD> | <TH>42</TH><TH>danRer5</TH><TD>Danio<BR>rerio</TD><TD>Zebrafish</TD> | ||
| Line 321: | Line 322: | ||
<TD>Wellcome Trust Sanger Institute, Zv7 assembly</TD> | <TD>Wellcome Trust Sanger Institute, Zv7 assembly</TD> | ||
<TD ALIGN=RIGHT>2007-09-05</TD> | <TD ALIGN=RIGHT>2007-09-05</TD> | ||
<TD ALIGN=RIGHT>N/A</TD><TD> | <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-26</TD><TD ALIGN=RIGHT>2.562%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>43</TH><TH>tetNig1</TH><TD>Tetraodon<BR>nigroviridis</TD><TD>Tetraodon</TD> | <TH>43</TH><TH>tetNig1</TH><TD>Tetraodon<BR>nigroviridis</TD><TD>Tetraodon</TD> | ||
Revision as of 23:18, 27 May 2009
see also
- Hg19 Genome size statistics
- Hg19 conservation lastz parameters
- Hg18 44way alignment
- Hg18 genome size statistics
- Hg18 44way blastz parameters
do not edit
This table is automatically generated off-line from the UCSC databases. Please do not edit it.
| UCSC db name |
Scientific name |
Common name |
assembly date |
source version |
Repeat Masker |
Window Masker |
chain on hg19 |
% of hg19 matched (chainLink table) |
|
|---|---|---|---|---|---|---|---|---|---|
| 01 | hg19 | Homo sapiens | Human | Feb. 2009 | GRCh37 Genome Reference Consortium Human Reference 37 (GCA_000001405.1) | 2009-04-24 | N/A | N/A | N/A |
| 02 | panTro2 | Pan troglodytes | Chimp | Mar. 2006 | Washington University Build 2 Version 1 | 2006-03-24 | N/A | 2009-03-20 | 94.846% |
| 03 | gorGor1 | Gorilla gorilla gorilla | Gorilla | Oct. 2008 | Sanger Institute Oct 2008 (NCBI project 31265, CABD01000000) | 2008-11-03 | N/A | 2009-03-22 | 59.484% |
| 04 | ponAbe2 | Pongo pygmaeus abelii | Orangutan | July 2007 | WUSTL 3.0 | 2007-09-15 | N/A | 2009-05-14 | 91.350% |
| 05 | rheMac2 | Macaca mulatta | Rhesus | Jan. 2006 | Venter Inst./Baylor/WashU Merged assembly Jan 2006 v1 edit4 | 2006-01-30 | N/A | 2009-05-14 | 82.744% |
| 06 | papHam1 | Papio hamadryas | Baboon | Nov. 2008 | Baylor BCM HGSC Pham_1.0 | 2009-05-13 | N/A | 2009-05-20 | 82.810% |
| 07 | calJac1 | Callithrix jacchus | Marmoset | June 2007 | WUSTL 2.0.2 | 2007-08-23 | N/A | 2009-05-14 | 70.860% |
| 08 | tarSyr1 | Tarsius syrichta | Tarsier | Aug. 2008 | Broad Institute tarSyr1 (NCBI project 20335, ABRT000000000) | 2008-10-15 | N/A | 2009-05-15 | 47.830% |
| 09 | otoGar1 | Otolemur garnettii | Bushbaby | Dec. 2006 | Broad version 1 (NCBI project 16955, AAQR00000000) | 2006-12-20 | N/A | 2009-05-15 | 43.644% |
| 10 | micMur1 | Microcebus murinus | Mouse lemur | Jun. 2003 | Broad Institute micMur1 (NCBI project 19967, ABDC00000000) | 2008-08-03 | N/A | 2009-05-22 | 46.519% |
| 11 | tupBel1 | Tupaia belangeri | TreeShrew | Dec. 2006 | Broad Institute tupBel1 (NCBI project 13971, AAPY01000000) | 2008-10-15 | N/A | N/A | N/A |
| 12 | sorAra1 | Sorex araneus | Shrew | June 2006 | Broad Institute sorAra1 (Draft_v2) | 2008-10-20 | 2008-10-21 | N/A | N/A |
| 13 | mm9 | Mus musculus | Mouse | July 2007 | NCBI Build 37 | 2007-07-20 | N/A | 2009-05-13 | 35.299% |
| 14 | rn4 | Rattus norvegicus | Rat | Nov. 2004 | Baylor HGSC v. 3.4 | 2006-03-16 | N/A | 2009-05-13 | 32.879% |
| 15 | speTri1 | Spermophilus tridecemlineatus | Squirrel | Feb. 2008 | Broad Institute speTri1 | 2008-08-03 | N/A | 2009-05-15 | 35.712% |
| 16 | cavPor3 | Cavia porcellus | Guinea Pig | Feb. 2008 | Broad Institute cavPor3 | 2008-04-05 | 2008-04-08 | 2009-05-22 | N/A |
| 17 | oryCun1 | Oryctolagus cuniculus | Rabbit | May 2005 | Broad May 2005 | 2005-05-22 | N/A | N/A | N/A |
| 18 | ochPri2 | Ochotona princeps | Pika | Jul. 2008 | Broad Institute ochPri2 | 2008-07-28 | N/A | N/A | N/A |
| 19 | eriEur1 | Erinaceus europaeus | Hedgehog | June 2006 | Broad Institute eriEur1 (Draft_v1, NCBI project 12575) | 2008-10-21 | 2008-10-21 | N/A | N/A |
| 20 | felCat3 | Felis catus | Cat | Mar. 2006 | Broad Release 3 | 2006-10-16 | N/A | 2009-05-14 | 35.717% |
| 21 | canFam2 | Canis lupus familiaris | Dog | May 2005 | Broad Institute v. 2.0 | 2005-07-10 | N/A | 2009-05-14 | 52.879% |
| 22 | equCab2 | Equus caballus | Horse | Sep. 2007 | Broad Institute EquCab2 | 2008-04-03 | N/A | 2009-05-22 | 57.051% |
| 23 | vicPac1 | Vicugna pacos | Alpaca | Jul. 2008 | Broad Institute vicPac1 | 2008-10-17 | N/A | N/A | N/A |
| 24 | pteVam1 | Pteropus vampyrus | Megabat | Jul. 2008 | Broad Institute pteVam1 (NCBI project 20325, ABRP01000000) | 2008-10-15 | N/A | 2009-05-21 | 45.416% |
| 25 | myoLuc1 | Myotis lucifugus | Microbat | Mar. 2006 | Broad Institute myoLuc1 | 2008-07-29 | N/A | N/A | N/A |
| 26 | turTru1 | Tursiops truncatus | Dolphin | Feb. 2008 | Broad Institute turTru1 (NCBI project 20367, ABRN01000000) | 2008-10-15 | N/A | N/A | N/A |
| 27 | bosTau4 | Bos taurus | Cow | Oct. 2007 | Baylor Release 4.0 | 2008-03-10 | N/A | 2009-05-21 | 46.507% |
| 28 | choHof1 | Choloepus hoffmanni | Sloth | Jul. 2008 | Broad Institute choHof1 | 2008-10-16 | N/A | 2009-05-26 | 34.376% |
| 29 | dipOrd1 | Dipodomys ordii | Kangaroo rat | Jul. 2008 | Broad Institute dipOrd1 (NCBI project 20385, ABRO01000000) | 2008-10-15 | N/A | N/A | N/A |
| 30 | proCap1 | Procavia capensis | Rock hyrax | Jul. 2008 | Broad Institute proCap1 (NCBI project 13972, ABRQ01000000) | 2008-10-16 | N/A | 2009-05-26 | 30.864% |
| 31 | macEug1 | Macropus eugenii | Wallaby | Nov. 2007 | Baylor Release 1.0 | N/A | 2008-12-26 | N/A | N/A |
| 32 | dasNov1 | Dasypus novemcinctus | Armadillo | May 2005 | Broad May 2005 | 2005-05-23 | N/A | N/A | N/A |
| 33 | echTel1 | Echinops telfairi | Tenrec | July 2005 | Broad July 2005 | 2005-08-04 | N/A | N/A | N/A |
| 34 | loxAfr2 | Loxodonta africana | Elephant | Jul. 2008 | Broad Institute loxAfr2 (NCBI project 12569, AAGU02000000) | 2008-10-07 | N/A | N/A | N/A |
| 35 | dasNov2 | Dasypus novemcinctus | Armadillo | Jul. 2008 | Broad Institute dasNov2 (NCBI project 12594, AAGV020000000) | 2008-10-07 | N/A | 2009-05-27 | N/A |
| 36 | monDom5 | Monodelphis domestica | Opossum | Oct. 2006 | Broad Institute monDom5 (NCBI project 12561, accession AAFR03000000) | 2008-11-26 | 2008-12-02 | N/A | N/A |
| 37 | ornAna1 | Ornithorhynchus anatinus | Platypus | Mar. 2007 | WUSTL version 5.0.1 | 2007-07-20 | N/A | 2009-05-27 | 7.627% |
| 38 | galGal3 | Gallus gallus | Chicken | May 2006 | Chicken Genome Sequencing Consortium May 2006 release | 2006-05-18 | 2007-01-02 | 2009-05-14 | 3.591% |
| 39 | taeGut1 | Taeniopygia guttata | Zebra finch | Jul. 2008 | Washington University taeGut1 | 2009-02-04 | 2008-08-05 | 2009-05-26 | 3.496% |
| 40 | anoCar1 | Anolis carolinensis | Lizard | Feb. 2007 | Broad Institute AnoCar (1.0) | 2007-03-07 | 2007-02-16 | N/A | N/A |
| 41 | xenTro2 | Xenopus tropicalis | X. tropicalis | Aug. 2005 | JGI v4.1 | 2006-04-17 | 2007-02-20 | 2009-05-27 | 3.176% |
| 42 | danRer5 | Danio rerio | Zebrafish | July 2007 | Wellcome Trust Sanger Institute, Zv7 assembly | 2007-09-05 | N/A | 2009-05-26 | 2.562% |
| 43 | tetNig1 | Tetraodon nigroviridis | Tetraodon | Feb. 2004 | Genoscope and Broad Institute V7 (NCBI project 12350, CAAE01000000) | 2004-08-17 | 2006-12-05 | 2009-05-14 | 2.003% |
| 44 | fr2 | Takifugu rubripes | Fugu | Oct. 2004 | JGI V4.0 | 2007-03-07 | 2007-01-22 | 2009-05-20 | 1.702% |
| 45 | gasAcu1 | Gasterosteus aculeatus | Stickleback | Feb. 2006 | Broad Institute gasAcu1 (1.0) (NCBI project 13579, AANH01000000) | 2006-10-17 | 2006-12-05 | 2009-05-14 | 1.916% |
| 46 | oryLat2 | Oryzias latipes | Medaka | Oct. 2005 | NIG and Tokyo Univ MEDAKA1 (NCBI project 16702, BAAF04000000) | 2008-08-12 | 2008-08-14 | 2009-05-22 | 1.849% |
| 47 | petMar1 | Petromyzon marinus | Lamprey | Mar. 2007 | WUSTL v.3.0 (March 2007) | N/A | 2008-01-28 | 2009-05-14 | 1.082% |
