Hg19 conservation lastz parameters: Difference between revisions

From genomewiki
Jump to navigationJump to search
m (initial page header)
 
(initial table contents)
Line 4: Line 4:
<LI>[[Hg19 Genome size statistics]]</LI>
<LI>[[Hg19 Genome size statistics]]</LI>
<LI>[[Hg19 conservation alignment]]</LI>
<LI>[[Hg19 conservation alignment]]</LI>
<LI>[[Hg18 blastz parameters]]</LI>
<LI>[[Hg18 44way blastz parameters]]</LI>
<LI>[[Genome size statistics|Hg18 Genome size statistics]]</LI>
<LI>[[Genome size statistics|Hg18 Genome size statistics]]</LI>
<LI>[[Hg18 44way alignment]]</LI>
<LI>[[Hg18 44way alignment]]</LI>
Line 10: Line 10:


==do not edit, automatically generated table==
==do not edit, automatically generated table==
<TABLE BORDER=1>
<TR><TH>query</TH>
  <TH>abridged<BR>repeats(no)</TH>
  <TH>M(40M)</TH><TH>K(3000)</TH>
  <TH>L(3000)</TH><TH>Q</TH><TH>Y(9400)</TH>
  <TH>program<BR>run</TH><TH>E(30)</TH><TH>H(0)</TH>
  <TH>O(400)</TH><TH>T(1)</TH>
  <TH>chain&nbsp;table<BR>date</TH>
  <TH>%&nbsp;of&nbsp;hg19<BR>matched<BR>(chainLink&nbsp;table)</TH>
</TR>
<TR>
  <TH>Chimp&nbsp;panTro2</TH>
  <TD>no</TD><TD>254</TD><TD>4500</TD><TD>3000</TD><TD>human_chimp.v2.q</TD>
  <TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>0</TD><TD>600</TD><TD>2</TD>
  <TD>2009-03-20</TD><TD ALIGN=RIGHT>94.846%</TD>
</TR><TR>
  <TH>Gorilla&nbsp;gorGor1</TH>
  <TD>no</TD><TD>254</TD><TD>4500</TD><TD>3000</TD><TD>human_chimp.v2.q</TD>
  <TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>0</TD><TD>600</TD><TD>2</TD>
  <TD>2009-03-22</TD><TD ALIGN=RIGHT>59.484%</TD>
</TR><TR>
  <TH>Orangutan&nbsp;ponAbe2</TH>
  <TD COLSPAN=13 ALIGN=center>TBD</TD>
</TR><TR>
  <TH>Rhesus&nbsp;rheMac2</TH>
  <TD>no</TD><TD>254</TD><TD>4500</TD><TD>3000</TD><TD>human_chimp.v2.q</TD>
  <TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>0</TD><TD>600</TD><TD>2</TD>
  <TD>in progress</TD><TD ALIGN=RIGHT>in progress</TD>
</TR><TR>
  <TH>Baboon&nbsp;papHam1</TH>
  <TD COLSPAN=13 ALIGN=center>TBD</TD>
</TR><TR>
  <TH>Marmoset&nbsp;calJac1</TH>
  <TD COLSPAN=13 ALIGN=center>TBD</TD>
</TR><TR>
  <TH>Bushbaby&nbsp;otoGar1</TH>
  <TD COLSPAN=13 ALIGN=center>TBD</TD>
</TR><TR>
  <TH>Mouse lemur&nbsp;micMur1</TH>
  <TD COLSPAN=13 ALIGN=center>TBD</TD>
</TR><TR>
  <TH>TreeShrew&nbsp;tupBel1</TH>
  <TD COLSPAN=13 ALIGN=center>TBD</TD>
</TR><TR>
  <TH>Shrew&nbsp;sorAra1</TH>
  <TD COLSPAN=13 ALIGN=center>TBD</TD>
</TR><TR>
  <TH>Mouse&nbsp;mm9</TH>
  <TD>yes</TD><TD>40M</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
  <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
  <TD>2009-05-13</TD><TD ALIGN=RIGHT>in progress</TD>
</TR><TR>
  <TH>Rat&nbsp;rn4</TH>
  <TD>yes</TD><TD>40M</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
  <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
  <TD>in progress</TD><TD ALIGN=RIGHT>in progress</TD>
</TR><TR>
  <TH>Squirrel&nbsp;speTri1</TH>
  <TD COLSPAN=13 ALIGN=center>TBD</TD>
</TR><TR>
  <TH>Guinea Pig&nbsp;cavPor3</TH>
  <TD COLSPAN=13 ALIGN=center>TBD</TD>
</TR><TR>
  <TH>Rabbit&nbsp;oryCun1</TH>
  <TD COLSPAN=13 ALIGN=center>TBD</TD>
</TR><TR>
  <TH>Pika&nbsp;ochPri2</TH>
  <TD COLSPAN=13 ALIGN=center>TBD</TD>
</TR><TR>
  <TH>Hedgehog&nbsp;eriEur1</TH>
  <TD COLSPAN=13 ALIGN=center>TBD</TD>
</TR><TR>
  <TH>Cat&nbsp;felCat3</TH>
  <TD COLSPAN=13 ALIGN=center>TBD</TD>
</TR><TR>
  <TH>Dog&nbsp;canFam2</TH>
  <TD>yes</TD><TD>40M</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
  <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
  <TD>2009-05-13</TD><TD ALIGN=RIGHT>in progress</TD>
</TR><TR>
  <TH>Horse&nbsp;equCab2</TH>
  <TD COLSPAN=13 ALIGN=center>TBD</TD>
</TR><TR>
  <TH>Alpaca&nbsp;vicPac1</TH>
  <TD COLSPAN=13 ALIGN=center>TBD</TD>
</TR><TR>
  <TH>Megabat&nbsp;pteVam1</TH>
  <TD COLSPAN=13 ALIGN=center>TBD</TD>
</TR><TR>
  <TH>Microbat&nbsp;myoLuc1</TH>
  <TD COLSPAN=13 ALIGN=center>TBD</TD>
</TR><TR>
  <TH>Dolphin&nbsp;turTru1</TH>
  <TD COLSPAN=13 ALIGN=center>TBD</TD>
</TR><TR>
  <TH>Cow&nbsp;bosTau4</TH>
  <TD COLSPAN=13 ALIGN=center>TBD</TD>
</TR><TR>
  <TH>Sloth&nbsp;choHof1</TH>
  <TD COLSPAN=13 ALIGN=center>TBD</TD>
</TR><TR>
  <TH>Tarsier&nbsp;tarSyr1</TH>
  <TD COLSPAN=13 ALIGN=center>TBD</TD>
</TR><TR>
  <TH>Kangaroo rat&nbsp;dipOrd1</TH>
  <TD COLSPAN=13 ALIGN=center>TBD</TD>
</TR><TR>
  <TH>Rock hyrax&nbsp;proCap1</TH>
  <TD COLSPAN=13 ALIGN=center>TBD</TD>
</TR><TR>
  <TH>Wallaby&nbsp;macEug1</TH>
  <TD COLSPAN=13 ALIGN=center>TBD</TD>
</TR><TR>
  <TH>Armadillo&nbsp;dasNov1</TH>
  <TD COLSPAN=13 ALIGN=center>TBD</TD>
</TR><TR>
  <TH>Tenrec&nbsp;echTel1</TH>
  <TD COLSPAN=13 ALIGN=center>TBD</TD>
</TR><TR>
  <TH>Elephant&nbsp;loxAfr2</TH>
  <TD COLSPAN=13 ALIGN=center>TBD</TD>
</TR><TR>
  <TH>Armadillo&nbsp;dasNov2</TH>
  <TD COLSPAN=13 ALIGN=center>TBD</TD>
</TR><TR>
  <TH>Opossum&nbsp;monDom5</TH>
  <TD COLSPAN=13 ALIGN=center>TBD</TD>
</TR><TR>
  <TH>Platypus&nbsp;ornAna1</TH>
  <TD COLSPAN=13 ALIGN=center>TBD</TD>
</TR><TR>
  <TH>Chicken&nbsp;galGal3</TH>
  <TD>yes</TD><TD>40M</TD><TD>2200</TD><TD>10000</TD><TD>HoxD55.q</TD>
  <TD>3400</TD><TD>lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>in progress</TD><TD ALIGN=RIGHT>in progress</TD>
</TR><TR>
  <TH>Zebra finch&nbsp;taeGut1</TH>
  <TD COLSPAN=13 ALIGN=center>TBD</TD>
</TR><TR>
  <TH>Lizard&nbsp;anoCar1</TH>
  <TD COLSPAN=13 ALIGN=center>TBD</TD>
</TR><TR>
  <TH>X. tropicalis&nbsp;xenTro2</TH>
  <TD COLSPAN=13 ALIGN=center>TBD</TD>
</TR><TR>
  <TH>Zebrafish&nbsp;danRer5</TH>
  <TD COLSPAN=13 ALIGN=center>TBD</TD>
</TR><TR>
  <TH>Tetraodon&nbsp;tetNig1</TH>
  <TD COLSPAN=13 ALIGN=center>TBD</TD>
</TR><TR>
  <TH>Fugu&nbsp;fr2</TH>
  <TD COLSPAN=13 ALIGN=center>TBD</TD>
</TR><TR>
  <TH>Stickleback&nbsp;gasAcu1</TH>
  <TD COLSPAN=13 ALIGN=center>TBD</TD>
</TR><TR>
  <TH>Medaka&nbsp;oryLat2</TH>
  <TD COLSPAN=13 ALIGN=center>TBD</TD>
</TR><TR>
  <TH>Lamprey&nbsp;petMar1</TH>
  <TD COLSPAN=13 ALIGN=center>TBD</TD>
</TR>
</TABLE>

Revision as of 18:52, 13 May 2009

See Also:

do not edit, automatically generated table

query abridged
repeats(no)
M(40M)K(3000) L(3000)QY(9400) program
run
E(30)H(0) O(400)T(1) chain table
date
% of hg19
matched
(chainLink table)
Chimp panTro2 no25445003000human_chimp.v2.q 15000lastz15006002 2009-03-2094.846%
Gorilla gorGor1 no25445003000human_chimp.v2.q 15000lastz15006002 2009-03-2259.484%
Orangutan ponAbe2 TBD
Rhesus rheMac2 no25445003000human_chimp.v2.q 15000lastz15006002 in progressin progress
Baboon papHam1 TBD
Marmoset calJac1 TBD
Bushbaby otoGar1 TBD
Mouse lemur micMur1 TBD
TreeShrew tupBel1 TBD
Shrew sorAra1 TBD
Mouse mm9 yes40M30003000default 9400lastz3004001 2009-05-13in progress
Rat rn4 yes40M30003000default 9400lastz3004001 in progressin progress
Squirrel speTri1 TBD
Guinea Pig cavPor3 TBD
Rabbit oryCun1 TBD
Pika ochPri2 TBD
Hedgehog eriEur1 TBD
Cat felCat3 TBD
Dog canFam2 yes40M30003000default 9400lastz3004001 2009-05-13in progress
Horse equCab2 TBD
Alpaca vicPac1 TBD
Megabat pteVam1 TBD
Microbat myoLuc1 TBD
Dolphin turTru1 TBD
Cow bosTau4 TBD
Sloth choHof1 TBD
Tarsier tarSyr1 TBD
Kangaroo rat dipOrd1 TBD
Rock hyrax proCap1 TBD
Wallaby macEug1 TBD
Armadillo dasNov1 TBD
Tenrec echTel1 TBD
Elephant loxAfr2 TBD
Armadillo dasNov2 TBD
Opossum monDom5 TBD
Platypus ornAna1 TBD
Chicken galGal3 yes40M220010000HoxD55.q 3400lastz3020004001 in progressin progress
Zebra finch taeGut1 TBD
Lizard anoCar1 TBD
X. tropicalis xenTro2 TBD
Zebrafish danRer5 TBD
Tetraodon tetNig1 TBD
Fugu fr2 TBD
Stickleback gasAcu1 TBD
Medaka oryLat2 TBD
Lamprey petMar1 TBD