Hg19 conservation lastz parameters: Difference between revisions

Revision as of 18:52, 13 May 2009

do not edit, automatically generated table

query	abridged repeats(no)	M(40M)	K(3000)	L(3000)	Q	Y(9400)	program run	E(30)	H(0)	O(400)	T(1)	chain table date	% of hg19 matched (chainLink table)
Chimp panTro2	no	254	4500	3000	human_chimp.v2.q	15000	lastz	150	0	600	2	2009-03-20	94.846%
Gorilla gorGor1	no	254	4500	3000	human_chimp.v2.q	15000	lastz	150	0	600	2	2009-03-22	59.484%
Orangutan ponAbe2	TBD
Rhesus rheMac2	no	254	4500	3000	human_chimp.v2.q	15000	lastz	150	0	600	2	in progress	in progress
Baboon papHam1	TBD
Marmoset calJac1	TBD
Bushbaby otoGar1	TBD
Mouse lemur micMur1	TBD
TreeShrew tupBel1	TBD
Shrew sorAra1	TBD
Mouse mm9	yes	40M	3000	3000	default	9400	lastz	30	0	400	1	2009-05-13	in progress
Rat rn4	yes	40M	3000	3000	default	9400	lastz	30	0	400	1	in progress	in progress
Squirrel speTri1	TBD
Guinea Pig cavPor3	TBD
Rabbit oryCun1	TBD
Pika ochPri2	TBD
Hedgehog eriEur1	TBD
Cat felCat3	TBD
Dog canFam2	yes	40M	3000	3000	default	9400	lastz	30	0	400	1	2009-05-13	in 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	yes	40M	2200	10000	HoxD55.q	3400	lastz	30	2000	400	1	in progress	in 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

@@ Line 4: / Line 4: @@
 <LI>[[Hg19 Genome size statistics]]</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>[[Hg18 44way alignment]]</LI>
@@ Line 10: / Line 10: @@
 ==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>

Hg19 conservation lastz parameters: Difference between revisions

Revision as of 18:52, 13 May 2009

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