Hg19 conservation alignment: Difference between revisions

Latest revision as of 16:16, 8 October 2012

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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	GRCh37	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	micMur1	Microcebus murinus	Mouse lemur	Jul. 2007	Broad Institute micMur1 (NCBI project 19967, ABDC00000000)	2008-08-03	N/A	2009-05-22	46.519%
10	otoGar1	Otolemur garnettii	Bushbaby	Dec. 2006	Broad version 1 (NCBI project 16955, AAQR00000000)	2006-12-20	N/A	2009-05-15	43.644%
11	equCab2	Equus caballus	Horse	Sep. 2007	Broad Institute EquCab2	2008-04-03	N/A	2009-06-04	57.050%
12	tupBel1	Tupaia belangeri	Tree shrew	Dec. 2006	Broad Institute tupBel1 (NCBI project 13971, AAPY01000000)	2008-10-15	N/A	2009-06-01	36.156%
13	turTru1	Tursiops truncatus	Dolphin	Feb. 2008	Broad Institute turTru1 (NCBI project 20367, ABRN01000000)	2008-10-15	N/A	2009-06-04	48.398%
14	speTri1	Spermophilus tridecemlineatus	Squirrel	Feb. 2008	Broad Institute speTri1	2008-08-03	N/A	2009-06-04	35.713%
15	vicPac1	Vicugna pacos	Alpaca	Jul. 2008	Broad Institute vicPac1	2008-10-17	N/A	2009-06-04	39.399%
16	choHof1	Choloepus hoffmanni	Sloth	Jul. 2008	Broad Institute choHof1	2008-10-16	N/A	2009-06-05	34.377%
17	pteVam1	Pteropus vampyrus	Megabat	Jul. 2008	Broad Institute pteVam1 (NCBI project 20325, ABRP01000000)	2008-10-15	N/A	2009-06-04	45.414%
18	loxAfr3	Loxodonta africana	Elephant	Jul. 2009	Broad Institute loxAfr3 (NCBI project 12569, AAGU03000000)	2009-07-15	N/A	2009-07-22	46.636%
19	felCat3	Felis catus	Cat	Mar. 2006	Broad Release 3	2006-10-16	N/A	2009-06-04	35.713%
20	canFam2	Canis lupus familiaris	Dog	May 2005	Broad Institute v. 2.0	2005-07-10	N/A	2009-05-14	52.879%
21	dasNov2	Dasypus novemcinctus	Armadillo	Jul. 2008	Broad Institute dasNov2 (NCBI project 12594, AAGV020000000)	2008-10-07	N/A	2009-05-27	33.543%
22	oryCun2	Oryctolagus cuniculus	Rabbit	Apr. 2009	Broad Institute oryCun2 (NCBI project 12819, AAGW00000000)	2009-08-11	N/A	2009-08-12	44.317%
23	myoLuc1	Myotis lucifugus	Microbat	Mar. 2006	Broad Institute myoLuc1	2008-07-29	N/A	2009-06-04	33.174%
24	bosTau4	Bos taurus	Cow	Oct. 2007	Baylor Release 4.0	2008-03-10	N/A	2009-06-04	46.506%
25	cavPor3	Cavia porcellus	Guinea Pig	Feb. 2008	Broad Institute cavPor3	2008-04-05	2008-04-08	2009-06-06	43.680%
26	proCap1	Procavia capensis	Rock hyrax	Jul. 2008	Broad Institute proCap1 (NCBI project 13972, ABRQ01000000)	2008-10-16	N/A	2009-05-26	30.864%
27	dipOrd1	Dipodomys ordii	Kangaroo rat	Jul. 2008	Broad Institute dipOrd1 (NCBI project 20385, ABRO01000000)	2008-10-15	N/A	2009-05-29	27.161%
28	ochPri2	Ochotona princeps	Pika	Jul. 2008	Broad Institute ochPri2	2008-07-28	N/A	2009-05-30	27.768%
29	eriEur1	Erinaceus europaeus	Hedgehog	June 2006	Broad Institute eriEur1 (Draft_v1, NCBI project 12575)	2008-10-21	2008-10-21	2009-05-30	19.362%
30	echTel1	Echinops telfairi	Tenrec	July 2005	Broad July 2005	2005-08-04	N/A	2009-05-28	23.120%
31	mm9	Mus musculus	Mouse	July 2007	NCBI Build 37	2007-07-20	N/A	2009-05-13	35.299%
32	rn4	Rattus norvegicus	Rat	Nov. 2004	Baylor HGSC v. 3.4	2006-03-16	N/A	2009-05-13	32.879%
33	sorAra1	Sorex araneus	Shrew	June 2006	Broad Institute sorAra1 (Draft_v2)	2008-10-20	2008-10-21	2009-05-29	19.760%
34	macEug1	Macropus eugenii	Wallaby	Nov. 2007	Baylor Release 1.0	N/A	2008-12-26	2009-05-31	6.011%
35	monDom5	Monodelphis domestica	Opossum	Oct. 2006	Broad Institute monDom5 (NCBI project 12561, accession AAFR03000000)	2009-07-06	2008-12-02	2009-05-29	14.358%
36	ornAna1	Ornithorhynchus anatinus	Platypus	Mar. 2007	WUSTL version 5.0.1	2007-07-20	N/A	2009-05-27	7.627%
37	galGal3	Gallus gallus	Chicken	May 2006	Chicken Genome Sequencing Consortium May 2006 release	2006-05-18	2007-01-02	2009-05-14	3.591%
38	taeGut1	Taeniopygia guttata	Zebra finch	Jul. 2008	Washington University taeGut1	2009-02-04	2008-08-05	2009-05-26	3.496%
39	anoCar1	Anolis carolinensis	Lizard	Feb. 2007	Broad Institute AnoCar (1.0)	2007-03-07	2007-02-16	2009-05-30	3.591%
40	xenTro2	Xenopus tropicalis	X. tropicalis	Aug. 2005	JGI v4.1	2006-04-17	2007-02-20	2009-05-27	3.176%
41	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%
42	fr2	Takifugu rubripes	Fugu	Oct. 2004	JGI V4.0	2007-03-07	2007-01-22	2009-05-20	1.702%
43	danRer6	Danio rerio	Zebrafish	Dec. 2008	Wellcome Trust Sanger Institute, Zv8 assembly (CAAK00000000.5)	2009-06-29	N/A	2009-07-10	3.051%
44	tetNig2	Tetraodon nigroviridis	Tetraodon	Mar. 2007	Genoscope Tetraodon v8.0 (NCBI project 12350, CAAE01000000)	N/A	2009-08-07	2009-08-10	1.712%
45	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%
46	petMar1	Petromyzon marinus	Lamprey	Mar. 2007	WUSTL v.3.0 (March 2007)	N/A	2008-01-28	2009-05-14	1.082%

@@ Line 2: / Line 2: @@
 <UL>
-<LI>[[Hg19 Genome size statistics]]</LI>
+<LI>46-way [[Hg19 Genome size statistics]]</LI>
-<LI>[[Hg19 conservation lastz parameters]]</LI>
+<LI>46-way [[Hg19 conservation lastz parameters]]</LI>
-<LI>[[Hg18 44way alignment]]</LI>
+<LI>all other [[UCSC Multiple Alignments]]</LI>
-<LI>[[Genome size statistics|Hg18 genome size statistics]]</LI>
-<LI>[[Hg18 44way blastz parameters]]</LI>
 </UL>
@@ Line 32: / Line 30: @@
    <TH>01</TH><TH>hg19</TH><TD>Homo<BR>sapiens</TD><TD>Human</TD>
-   <TD>Feb.&nbsp;2009</TD>
+   <TD>GRCh37</TD>
    <TD>GRCh37 Genome Reference Consortium Human Reference 37 (GCA_000001405.1)</TD>
    <TD ALIGN=RIGHT>2009-04-24</TD>
@@ Line 88: / Line 86: @@
    <TH>09</TH><TH>micMur1</TH><TD>Microcebus<BR>murinus</TD><TD>Mouse&nbsp;lemur</TD>
-   <TD>Jun.&nbsp;2003</TD>
+   <TD>Jul.&nbsp;2007</TD>
    <TD>Broad Institute micMur1 (NCBI project 19967, ABDC00000000)</TD>
    <TD ALIGN=RIGHT>2008-08-03</TD>
@@ Line 107: / Line 105: @@
    <TD ALIGN=RIGHT>N/A</TD><TD>2009-06-04</TD><TD ALIGN=RIGHT>57.050%</TD>
 </TR><TR>
-   <TH>12</TH><TH>tupBel1</TH><TD>Tupaia<BR>belangeri</TD><TD>TreeShrew</TD>
+   <TH>12</TH><TH>tupBel1</TH><TD>Tupaia<BR>belangeri</TD><TD>Tree&nbsp;shrew</TD>
    <TD>Dec.&nbsp;2006</TD>
@@ Line 149: / Line 147: @@
    <TD ALIGN=RIGHT>N/A</TD><TD>2009-06-04</TD><TD ALIGN=RIGHT>45.414%</TD>
 </TR><TR>
-   <TH>18</TH><TH>loxAfr2</TH><TD>Loxodonta<BR>africana</TD><TD>Elephant</TD>
+   <TH>18</TH><TH>loxAfr3</TH><TD>Loxodonta<BR>africana</TD><TD>Elephant</TD>
-   <TD>Jul.&nbsp;2008</TD>
+   <TD>Jul.&nbsp;2009</TD>
-   <TD>Broad Institute loxAfr2 (NCBI project 12569, AAGU02000000)</TD>
+   <TD>Broad Institute loxAfr3 (NCBI project 12569, AAGU03000000)</TD>
-   <TD ALIGN=RIGHT>2008-10-07</TD>
+   <TD ALIGN=RIGHT>2009-07-15</TD>
-   <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-28</TD><TD ALIGN=RIGHT>35.153%</TD>
+   <TD ALIGN=RIGHT>N/A</TD><TD>2009-07-22</TD><TD ALIGN=RIGHT>46.636%</TD>
 </TR><TR>
    <TH>19</TH><TH>felCat3</TH><TD>Felis<BR>catus</TD><TD>Cat</TD>
@@ Line 177: / Line 175: @@
    <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-27</TD><TD ALIGN=RIGHT>33.543%</TD>
 </TR><TR>
-   <TH>22</TH><TH>oryCun1</TH><TD>Oryctolagus<BR>cuniculus</TD><TD>Rabbit</TD>
+   <TH>22</TH><TH>oryCun2</TH><TD>Oryctolagus<BR>cuniculus</TD><TD>Rabbit</TD>
-   <TD>May&nbsp;2005</TD>
+   <TD>Apr.&nbsp;2009</TD>
-   <TD>Broad May 2005</TD>
+   <TD>Broad Institute oryCun2 (NCBI project 12819, AAGW00000000)</TD>
-   <TD ALIGN=RIGHT>2005-05-22</TD>
+   <TD ALIGN=RIGHT>2009-08-11</TD>
-   <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-29</TD><TD ALIGN=RIGHT>33.676%</TD>
+   <TD ALIGN=RIGHT>N/A</TD><TD>2009-08-12</TD><TD ALIGN=RIGHT>44.317%</TD>
 </TR><TR>
    <TH>23</TH><TH>myoLuc1</TH><TD>Myotis<BR>lucifugus</TD><TD>Microbat</TD>
@@ Line 272: / Line 270: @@
    <TD>Oct.&nbsp;2006</TD>
    <TD>Broad Institute monDom5 (NCBI project 12561, accession AAFR03000000)</TD>
-   <TD ALIGN=RIGHT>2009-06-04</TD>
+   <TD ALIGN=RIGHT>2009-07-06</TD>
    <TD ALIGN=RIGHT>2008-12-02</TD><TD>2009-05-29</TD><TD ALIGN=RIGHT>14.358%</TD>
 </TR><TR>
@@ Line 324: / Line 322: @@
    <TD ALIGN=RIGHT>2007-01-22</TD><TD>2009-05-20</TD><TD ALIGN=RIGHT>1.702%</TD>
 </TR><TR>
-   <TH>43</TH><TH>danRer5</TH><TD>Danio<BR>rerio</TD><TD>Zebrafish</TD>
+   <TH>43</TH><TH>danRer6</TH><TD>Danio<BR>rerio</TD><TD>Zebrafish</TD>
-   <TD>July&nbsp;2007</TD>
+   <TD>Dec.&nbsp;2008</TD>
-   <TD>Wellcome Trust Sanger Institute, Zv7 assembly</TD>
+   <TD>Wellcome Trust Sanger Institute, Zv8 assembly (CAAK00000000.5)</TD>
-   <TD ALIGN=RIGHT>2007-09-05</TD>
+   <TD ALIGN=RIGHT>2009-06-29</TD>
-   <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-26</TD><TD ALIGN=RIGHT>2.562%</TD>
+   <TD ALIGN=RIGHT>N/A</TD><TD>2009-07-10</TD><TD ALIGN=RIGHT>3.051%</TD>
 </TR><TR>
-   <TH>44</TH><TH>tetNig1</TH><TD>Tetraodon<BR>nigroviridis</TD><TD>Tetraodon</TD>
+   <TH>44</TH><TH>tetNig2</TH><TD>Tetraodon<BR>nigroviridis</TD><TD>Tetraodon</TD>
-   <TD>Feb.&nbsp;2004</TD>
+   <TD>Mar.&nbsp;2007</TD>
-   <TD>Genoscope and Broad Institute V7 (NCBI project 12350, CAAE01000000)</TD>
+   <TD>Genoscope Tetraodon v8.0 (NCBI project 12350, CAAE01000000)</TD>
-   <TD ALIGN=RIGHT>2004-08-17</TD>
+   <TD ALIGN=RIGHT>N/A</TD>
-   <TD ALIGN=RIGHT>2006-12-05</TD><TD>2009-05-14</TD><TD ALIGN=RIGHT>2.003%</TD>
+   <TD ALIGN=RIGHT>2009-08-07</TD><TD>2009-08-10</TD><TD ALIGN=RIGHT>1.712%</TD>
 </TR><TR>
    <TH>45</TH><TH>oryLat2</TH><TD>Oryzias<BR>latipes</TD><TD>Medaka</TD>

Hg19 conservation alignment: Difference between revisions

Latest revision as of 16:16, 8 October 2012

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