Hg19 conservation lastz parameters: Difference between revisions
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<TH>L(3000)</TH><TH>Q</TH><TH>Y(9400)</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>program<BR>run</TH><TH>E(30)</TH><TH>H(0)</TH> | ||
<TH>O(400)</TH><TH>T(1)</TH> | <TH>O(400)</TH><TH>T(1)</TH> | ||
<TH>chain table<BR>date</TH> | <TH>chain table<BR>date</TH> | ||
<TH>% of hg19<BR>matched<BR>(chainLink table)</TH> | <TH>% of hg19<BR>matched<BR>(chainLink table)</TH> | ||
</TR> | </TR> | ||
<TR> | <TR> | ||
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<TD>no</TD><TD>254</TD><TD>4500</TD><TD>3000</TD><TD>human_chimp.v2.q</TD> | <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>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> | <TD>2009-03-20</TD><TD ALIGN=RIGHT>94.846%</TD> | ||
</TR><TR> | </TR><TR> | ||
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<TD>no</TD><TD>254</TD><TD>4500</TD><TD>3000</TD><TD>human_chimp.v2.q</TD> | <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>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> | <TD>2009-03-22</TD><TD ALIGN=RIGHT>59.484%</TD> | ||
</TR><TR> | </TR><TR> | ||
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<TD>no</TD><TD>254</TD><TD>4500</TD><TD>3000</TD><TD>human_chimp.v2.q</TD> | <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>15000</TD><TD>lastz</TD><TD>150</TD><TD>0</TD><TD>600</TD><TD>2</TD> | ||
<TD>2009-05-14</TD><TD ALIGN=RIGHT>91.350%</TD> | <TD>2009-05-14</TD><TD ALIGN=RIGHT>91.350%</TD> | ||
</TR><TR> | </TR><TR> | ||
| Line 41: | Line 46: | ||
<TD>no</TD><TD>254</TD><TD>4500</TD><TD>3000</TD><TD>human_chimp.v2.q</TD> | <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>15000</TD><TD>lastz</TD><TD>150</TD><TD>0</TD><TD>600</TD><TD>2</TD> | ||
<TD> | |||
<TD>2009-05-14</TD><TD ALIGN=RIGHT>82.744%</TD> | |||
</TR><TR> | </TR><TR> | ||
<TH>Baboon papHam1</TH> | <TH>Baboon papHam1</TH> | ||
<TD | <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> | </TR><TR> | ||
<TH>Marmoset calJac1</TH> | <TH>Marmoset calJac1</TH> | ||
<TD | <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>2009-05-14</TD><TD ALIGN=RIGHT>in progress</TD> | |||
</TR><TR> | |||
<TH>Tarsier tarSyr1</TH> | |||
<TD>no</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>2009-05-15</TD><TD ALIGN=RIGHT>in progress</TD> | |||
</TR><TR> | </TR><TR> | ||
<TH>Bushbaby otoGar1</TH> | <TH>Bushbaby otoGar1</TH> | ||
<TD | <TD>no</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>2009-05-15</TD><TD ALIGN=RIGHT>in progress</TD> | |||
</TR><TR> | </TR><TR> | ||
<TH>Mouse lemur micMur1</TH> | <TH>Mouse lemur micMur1</TH> | ||
<TD | <TD>no</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> | </TR><TR> | ||
<TH>TreeShrew tupBel1</TH> | <TH>TreeShrew tupBel1</TH> | ||
| Line 59: | Line 83: | ||
</TR><TR> | </TR><TR> | ||
<TH>Shrew sorAra1</TH> | <TH>Shrew sorAra1</TH> | ||
<TD COLSPAN=13 ALIGN=center>TBD</TD> | <TD COLSPAN=13 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR><TR> | ||
| Line 64: | Line 89: | ||
<TD>yes</TD><TD>40M</TD><TD>3000</TD><TD>3000</TD><TD>default</TD> | <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>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>35.299%</TD> | <TD>2009-05-13</TD><TD ALIGN=RIGHT>35.299%</TD> | ||
</TR><TR> | </TR><TR> | ||
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<TD>yes</TD><TD>40M</TD><TD>3000</TD><TD>3000</TD><TD>default</TD> | <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>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>32.879%</TD> | <TD>2009-05-13</TD><TD ALIGN=RIGHT>32.879%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>Squirrel speTri1</TH> | <TH>Squirrel speTri1</TH> | ||
<TD | <TD>no</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>2009-05-15</TD><TD ALIGN=RIGHT>35.712%</TD> | |||
</TR><TR> | </TR><TR> | ||
<TH>Guinea Pig cavPor3</TH> | <TH>Guinea Pig cavPor3</TH> | ||
<TD | <TD>no</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>2009-05-19</TD><TD ALIGN=RIGHT>N/A</TD> | |||
</TR><TR> | </TR><TR> | ||
<TH>Rabbit oryCun1</TH> | <TH>Rabbit oryCun1</TH> | ||
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</TR><TR> | </TR><TR> | ||
<TH>Pika ochPri2</TH> | <TH>Pika ochPri2</TH> | ||
<TD COLSPAN=13 ALIGN=center>TBD</TD> | <TD COLSPAN=13 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR><TR> | ||
| Line 88: | Line 122: | ||
<TH>Cat felCat3</TH> | <TH>Cat felCat3</TH> | ||
<TD>no</TD><TD>40M</TD><TD>3000</TD><TD>3000</TD><TD>default</TD> | <TD>no</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>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD> | ||
<TD> | <TD>2009-05-14</TD><TD ALIGN=RIGHT>35.717%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>Dog canFam2</TH> | <TH>Dog canFam2</TH> | ||
<TD>yes</TD><TD>40M</TD><TD>3000</TD><TD>3000</TD><TD>default</TD> | <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>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD> | ||
<TD>2009-05-14</TD><TD ALIGN=RIGHT>52.879%</TD> | <TD>2009-05-14</TD><TD ALIGN=RIGHT>52.879%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>Horse equCab2</TH> | <TH>Horse equCab2</TH> | ||
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<TD COLSPAN=13 ALIGN=center>TBD</TD> | <TD COLSPAN=13 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>Megabat pteVam1</TH> | <TH>Megabat pteVam1</TH> | ||
<TD COLSPAN=13 ALIGN=center>TBD</TD> | <TD COLSPAN=13 ALIGN=center>TBD</TD> | ||
| Line 109: | Line 147: | ||
</TR><TR> | </TR><TR> | ||
<TH>Dolphin turTru1</TH> | <TH>Dolphin turTru1</TH> | ||
<TD COLSPAN=13 ALIGN=center>TBD</TD> | <TD COLSPAN=13 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR><TR> | ||
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<TH>Sloth choHof1</TH> | <TH>Sloth choHof1</TH> | ||
<TD COLSPAN=13 ALIGN=center>TBD</TD> | <TD COLSPAN=13 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>Kangaroo rat dipOrd1</TH> | <TH>Kangaroo rat dipOrd1</TH> | ||
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<TD COLSPAN=13 ALIGN=center>TBD</TD> | <TD COLSPAN=13 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>Wallaby macEug1</TH> | <TH>Wallaby macEug1</TH> | ||
<TD COLSPAN=13 ALIGN=center>TBD</TD> | <TD COLSPAN=13 ALIGN=center>TBD</TD> | ||
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</TR><TR> | </TR><TR> | ||
<TH>Tenrec echTel1</TH> | <TH>Tenrec echTel1</TH> | ||
<TD COLSPAN=13 ALIGN=center>TBD</TD> | <TD COLSPAN=13 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR><TR> | ||
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<TH>Armadillo dasNov2</TH> | <TH>Armadillo dasNov2</TH> | ||
<TD COLSPAN=13 ALIGN=center>TBD</TD> | <TD COLSPAN=13 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>Opossum monDom5</TH> | <TH>Opossum monDom5</TH> | ||
| Line 147: | Line 187: | ||
<TD COLSPAN=13 ALIGN=center>TBD</TD> | <TD COLSPAN=13 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>Chicken galGal3</TH> | <TH>Chicken galGal3</TH> | ||
<TD>yes</TD><TD>40M</TD><TD>2200</TD><TD>10000</TD><TD>HoxD55.q</TD> | <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>3400</TD><TD>lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | ||
<TD>2009-05-14</TD><TD ALIGN=RIGHT> | |||
<TD>2009-05-14</TD><TD ALIGN=RIGHT>3.591%</TD> | |||
</TR><TR> | </TR><TR> | ||
<TH>Zebra finch taeGut1</TH> | <TH>Zebra finch taeGut1</TH> | ||
| Line 156: | Line 198: | ||
</TR><TR> | </TR><TR> | ||
<TH>Lizard anoCar1</TH> | <TH>Lizard anoCar1</TH> | ||
<TD COLSPAN=13 ALIGN=center>TBD</TD> | <TD COLSPAN=13 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR><TR> | ||
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<TH>Zebrafish danRer5</TH> | <TH>Zebrafish danRer5</TH> | ||
<TD COLSPAN=13 ALIGN=center>TBD</TD> | <TD COLSPAN=13 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>Tetraodon tetNig1</TH> | <TH>Tetraodon tetNig1</TH> | ||
<TD | <TD>no</TD><TD>50</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD> | ||
<TD>3400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD> | |||
<TD>2009-05-14</TD><TD ALIGN=RIGHT>2.003%</TD> | |||
</TR><TR> | </TR><TR> | ||
<TH>Fugu fr2</TH> | <TH>Fugu fr2</TH> | ||
<TD | <TD>no</TD><TD>50</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD> | ||
<TD>3400</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> | </TR><TR> | ||
<TH>Stickleback gasAcu1</TH> | <TH>Stickleback gasAcu1</TH> | ||
<TD | <TD>no</TD><TD>50</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD> | ||
<TD>3400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD> | |||
<TD>2009-05-14</TD><TD ALIGN=RIGHT>1.916%</TD> | |||
</TR><TR> | </TR><TR> | ||
<TH>Medaka oryLat2</TH> | <TH>Medaka oryLat2</TH> | ||
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</TR><TR> | </TR><TR> | ||
<TH>Lamprey petMar1</TH> | <TH>Lamprey petMar1</TH> | ||
<TD | <TD>no</TD><TD>50</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD> | ||
<TD>3400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD> | |||
<TD>2009-05-14</TD><TD ALIGN=RIGHT>in progress</TD> | |||
</TR> | </TR> | ||
</TABLE> | </TABLE> | ||
[[Category:Comparative Genomics]] | [[Category:Comparative Genomics]] | ||
Revision as of 23:27, 20 May 2009
See Also:
- Hg19 Genome size statistics
- Hg19 conservation alignment
- Hg19 Andy's alignment notes
- Hg18 44way blastz parameters
- Hg18 Genome size statistics
- Hg18 44way alignment
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 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz | 150 | 0 | 600 | 2 | 2009-05-14 | 91.350% |
| Rhesus rheMac2 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz | 150 | 0 | 600 | 2 | 2009-05-14 | 82.744% |
| Baboon papHam1 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz | 150 | 0 | 600 | 2 | in progress | in progress |
| Marmoset calJac1 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz | 150 | 0 | 600 | 2 | 2009-05-14 | in progress |
| Tarsier tarSyr1 | no | 40M | 3000 | 3000 | default | 9400 | lastz | 30 | 0 | 400 | 1 | 2009-05-15 | in progress |
| Bushbaby otoGar1 | no | 40M | 3000 | 3000 | default | 9400 | lastz | 30 | 0 | 400 | 1 | 2009-05-15 | in progress |
| Mouse lemur micMur1 | no | 40M | 3000 | 3000 | default | 9400 | lastz | 30 | 0 | 400 | 1 | in progress | in progress |
| TreeShrew tupBel1 | TBD | ||||||||||||
| Shrew sorAra1 | TBD | ||||||||||||
| Mouse mm9 | yes | 40M | 3000 | 3000 | default | 9400 | lastz | 30 | 0 | 400 | 1 | 2009-05-13 | 35.299% |
| Rat rn4 | yes | 40M | 3000 | 3000 | default | 9400 | lastz | 30 | 0 | 400 | 1 | 2009-05-13 | 32.879% |
| Squirrel speTri1 | no | 40M | 3000 | 3000 | default | 9400 | lastz | 30 | 0 | 400 | 1 | 2009-05-15 | 35.712% |
| Guinea Pig cavPor3 | no | 40M | 3000 | 3000 | default | 9400 | lastz | 30 | 0 | 400 | 1 | 2009-05-19 | N/A |
| Rabbit oryCun1 | TBD | ||||||||||||
| Pika ochPri2 | TBD | ||||||||||||
| Hedgehog eriEur1 | TBD | ||||||||||||
| Cat felCat3 | no | 40M | 3000 | 3000 | default | 9400 | lastz | 30 | 0 | 400 | 1 | 2009-05-14 | 35.717% |
| Dog canFam2 | yes | 40M | 3000 | 3000 | default | 9400 | lastz | 30 | 0 | 400 | 1 | 2009-05-14 | 52.879% |
| Horse equCab2 | TBD | ||||||||||||
| Alpaca vicPac1 | TBD | ||||||||||||
| Megabat pteVam1 | TBD | ||||||||||||
| Microbat myoLuc1 | TBD | ||||||||||||
| Dolphin turTru1 | TBD | ||||||||||||
| Cow bosTau4 | TBD | ||||||||||||
| Sloth choHof1 | 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 | 2009-05-14 | 3.591% |
| Zebra finch taeGut1 | TBD | ||||||||||||
| Lizard anoCar1 | TBD | ||||||||||||
| X. tropicalis xenTro2 | TBD | ||||||||||||
| Zebrafish danRer5 | TBD | ||||||||||||
| Tetraodon tetNig1 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz | 30 | 0 | 400 | 1 | 2009-05-14 | 2.003% |
| Fugu fr2 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz | 30 | 0 | 400 | 1 | in progress | in progress |
| Stickleback gasAcu1 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz | 30 | 0 | 400 | 1 | 2009-05-14 | 1.916% |
| Medaka oryLat2 | TBD | ||||||||||||
| Lamprey petMar1 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz | 30 | 0 | 400 | 1 | 2009-05-14 | in progress |
