PanTro3 Genome size statistics: Difference between revisions
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==see also== | |||
<UL> | <UL> | ||
<LI>[[PanTro3 conservation alignment]]</LI> | <LI>Chimp 12-way [[PanTro3 conservation alignment]]</LI> | ||
<LI>[[ | <LI>Chimp 12-way [[PanTro3 conservation lastz parameters]]</LI> | ||
<LI>all other [[UCSC Multiple Alignments]]</LI> | |||
<LI>[[ | |||
</UL> | </UL> | ||
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<LI>The N50 size is calculated directly from the UCSC chrom.sizes file which is the size of the chromosomes as seen in the UCSC genome browser</LI> | <LI>The N50 size is calculated directly from the UCSC chrom.sizes file which is the size of the chromosomes as seen in the UCSC genome browser</LI> | ||
<LI>% masked == masked either with WindowMasker or RepeatMasker plus TRF simple repeats</LI> | <LI>% masked == masked either with WindowMasker or RepeatMasker plus TRF simple repeats</LI> | ||
<LI>% of | <LI>% of panTro3 matched (chainLink table) == featureBits panTro3 chain<Db>Link == alignment coverage</LI> | ||
</UL> | </UL> | ||
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<TD ALIGN=CENTER>Human</TD><TH ALIGN=CENTER>20X</TH> | <TD ALIGN=CENTER>Human</TD><TH ALIGN=CENTER>20X</TH> | ||
<TH ALIGN=CENTER>146364022</TH> | <TH ALIGN=CENTER>146364022</TH> | ||
<TH ALIGN=CENTER> | <TH ALIGN=CENTER>SynetnicNet</TH><TD ALIGN=RIGHT>95.597%</TD> | ||
<TD ALIGN=RIGHT> | <TD ALIGN=RIGHT>5000</TD> | ||
<TD ALIGN=CENTER> | <TD ALIGN=CENTER>medium</TD></TR> | ||
<TR><TH ALIGN=RIGHT>03</TH><TH ALIGN=RIGHT>[http://genome.wustl.edu/genomes/view/pongo_abelii/ ponAbe2]</TH> | <TR><TH ALIGN=RIGHT>03</TH><TH ALIGN=RIGHT>[http://genome.wustl.edu/genomes/view/pongo_abelii/ ponAbe2]</TH> | ||
<TH ALIGN=RIGHT>55</TH> | <TH ALIGN=RIGHT>55</TH> | ||
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<TD ALIGN=CENTER>Orangutan</TD><TH ALIGN=CENTER>6X</TH> | <TD ALIGN=CENTER>Orangutan</TD><TH ALIGN=CENTER>6X</TH> | ||
<TH ALIGN=CENTER>135191526</TH> | <TH ALIGN=CENTER>135191526</TH> | ||
<TH ALIGN=CENTER> | <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>89.586%</TD> | ||
<TD ALIGN=RIGHT>5000</TD> | <TD ALIGN=RIGHT>5000</TD> | ||
<TD ALIGN=CENTER>medium</TD></TR> | <TD ALIGN=CENTER>medium</TD></TR> | ||
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<TD ALIGN=CENTER>Rhesus</TD><TH ALIGN=CENTER>5.1X</TH> | <TD ALIGN=CENTER>Rhesus</TD><TH ALIGN=CENTER>5.1X</TH> | ||
<TH ALIGN=CENTER>153947521</TH> | <TH ALIGN=CENTER>153947521</TH> | ||
<TH ALIGN=CENTER> | <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>81.342%</TD> | ||
<TD ALIGN=RIGHT>5000</TD> | <TD ALIGN=RIGHT>5000</TD> | ||
<TD ALIGN=CENTER>medium</TD></TR> | <TD ALIGN=CENTER>medium</TD></TR> | ||
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<TD ALIGN=CENTER>Marmoset</TD><TH ALIGN=CENTER>6X</TH> | <TD ALIGN=CENTER>Marmoset</TD><TH ALIGN=CENTER>6X</TH> | ||
<TH ALIGN=CENTER>132174527</TH> | <TH ALIGN=CENTER>132174527</TH> | ||
<TH ALIGN=CENTER> | <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>69.662%</TD> | ||
<TD ALIGN=RIGHT>5000</TD> | <TD ALIGN=RIGHT>5000</TD> | ||
<TD ALIGN=CENTER>medium</TD></TR> | <TD ALIGN=CENTER>medium</TD></TR> | ||
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<TD ALIGN=CENTER>Horse</TD><TH ALIGN=CENTER>6.8X</TH> | <TD ALIGN=CENTER>Horse</TD><TH ALIGN=CENTER>6.8X</TH> | ||
<TH ALIGN=CENTER>91571448</TH> | <TH ALIGN=CENTER>91571448</TH> | ||
<TH ALIGN=CENTER> | <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>56.504%</TD> | ||
<TD ALIGN=RIGHT>3000</TD> | <TD ALIGN=RIGHT>3000</TD> | ||
<TD ALIGN=CENTER>medium</TD></TR> | <TD ALIGN=CENTER>medium</TD></TR> | ||
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<TD ALIGN=CENTER>Dog</TD><TH ALIGN=CENTER>7.6X</TH> | <TD ALIGN=CENTER>Dog</TD><TH ALIGN=CENTER>7.6X</TH> | ||
<TH ALIGN=CENTER>67211953</TH> | <TH ALIGN=CENTER>67211953</TH> | ||
<TH ALIGN=CENTER> | <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>51.588%</TD> | ||
<TD ALIGN=RIGHT>3000</TD> | <TD ALIGN=RIGHT>3000</TD> | ||
<TD ALIGN=CENTER>medium</TD></TR> | <TD ALIGN=CENTER>medium</TD></TR> | ||
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<TD ALIGN=CENTER>Mouse</TD><TH ALIGN=CENTER>20X</TH> | <TD ALIGN=CENTER>Mouse</TD><TH ALIGN=CENTER>20X</TH> | ||
<TH ALIGN=CENTER>131738871</TH> | <TH ALIGN=CENTER>131738871</TH> | ||
<TH ALIGN=CENTER> | <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>32.044%</TD> | ||
<TD ALIGN=RIGHT>3000</TD> | <TD ALIGN=RIGHT>3000</TD> | ||
<TD ALIGN=CENTER>medium</TD></TR> | <TD ALIGN=CENTER>medium</TD></TR> | ||
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<TD ALIGN=CENTER>Rat</TD><TH ALIGN=CENTER>20X</TH> | <TD ALIGN=CENTER>Rat</TD><TH ALIGN=CENTER>20X</TH> | ||
<TH ALIGN=CENTER>143002779</TH> | <TH ALIGN=CENTER>143002779</TH> | ||
<TH ALIGN=CENTER> | <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>30.350%</TD> | ||
<TD ALIGN=RIGHT>3000</TD> | <TD ALIGN=RIGHT>3000</TD> | ||
<TD ALIGN=CENTER>medium</TD></TR> | <TD ALIGN=CENTER>medium</TD></TR> | ||
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<TD ALIGN=CENTER>Opossum</TD><TH ALIGN=CENTER>6.8X</TH> | <TD ALIGN=CENTER>Opossum</TD><TH ALIGN=CENTER>6.8X</TH> | ||
<TH ALIGN=CENTER>527952102</TH> | <TH ALIGN=CENTER>527952102</TH> | ||
<TH ALIGN=CENTER> | <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>13.743%</TD> | ||
<TD ALIGN=RIGHT>5000</TD> | <TD ALIGN=RIGHT>5000</TD> | ||
<TD ALIGN=CENTER>loose</TD></TR> | <TD ALIGN=CENTER>loose</TD></TR> | ||
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<TD ALIGN=CENTER>Chicken</TD><TH ALIGN=CENTER>6.6X</TH> | <TD ALIGN=CENTER>Chicken</TD><TH ALIGN=CENTER>6.6X</TH> | ||
<TH ALIGN=CENTER>94230402</TH> | <TH ALIGN=CENTER>94230402</TH> | ||
<TH ALIGN=CENTER> | <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>4.557%</TD> | ||
<TD ALIGN=RIGHT>5000</TD> | <TD ALIGN=RIGHT>5000</TD> | ||
<TD ALIGN=CENTER>loose</TD></TR> | <TD ALIGN=CENTER>loose</TD></TR> | ||
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<TD ALIGN=CENTER>Zebrafish</TD><TH ALIGN=CENTER>30X</TH> | <TD ALIGN=CENTER>Zebrafish</TD><TH ALIGN=CENTER>30X</TH> | ||
<TH ALIGN=CENTER>54093808</TH> | <TH ALIGN=CENTER>54093808</TH> | ||
<TH ALIGN=CENTER> | <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>2.558%</TD> | ||
<TD ALIGN=RIGHT>5000</TD> | <TD ALIGN=RIGHT>5000</TD> | ||
<TD ALIGN=CENTER>loose</TD></TR> | <TD ALIGN=CENTER>loose</TD></TR> | ||
</TABLE> | </TABLE> | ||
Latest revision as of 22:37, 18 May 2011
see also
- Chimp 12-way PanTro3 conservation alignment
- Chimp 12-way PanTro3 conservation lastz parameters
- all other UCSC Multiple Alignments
statistics collected from UCSC 2bit files
- The external links from the UCSC database name go to the sequencing center information pages for this genome
- N bases == unknown bases in the assembly marked by 'N'
- non-N bases == called bases in the assembly
- total size == all bases in assembly, N and non-N
- The coverage numbers are taken directly from information README files from the sequencing center
- The N50 size is calculated directly from the UCSC chrom.sizes file which is the size of the chromosomes as seen in the UCSC genome browser
- % masked == masked either with WindowMasker or RepeatMasker plus TRF simple repeats
- % of panTro3 matched (chainLink table) == featureBits panTro3 chain<Db>Link == alignment coverage
do not edit, automatically generated table
| order count |
ucsc db name |
chrom count |
total size |
non-N bases |
N base count |
% masked | common name | coverage | N50 chrom.sizes |
alignment type | % of panTro3 matched (chainLink table) |
chain minScore |
chain linearGap |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 01 | panTro3 | 24,132 | 3,307,960,432 | 2,900,529,764 | 407,430,668 | % 50.64 | Chimp | 6X | 143986469 | N/A | N/A | 1000 | N/A |
| 02 | hg19 | 93 | 3,137,161,264 | 2,897,310,462 | 239,850,802 | % 50.63 | Human | 20X | 146364022 | SynetnicNet | 95.597% | 5000 | medium |
| 03 | ponAbe2 | 55 | 3,446,771,396 | 3,093,543,172 | 353,228,224 | % 50.89 | Orangutan | 6X | 135191526 | SyntenicNet | 89.586% | 5000 | medium |
| 04 | rheMac2 | 22 | 2,864,106,071 | 2,646,668,809 | 217,437,262 | % 48.28 | Rhesus | 5.1X | 153947521 | SyntenicNet | 81.342% | 5000 | medium |
| 05 | calJac3 | 14,205 | 2,914,958,544 | 2,752,505,800 | 162,452,744 | % 47.71 | Marmoset | 6X | 132174527 | SyntenicNet | 69.662% | 5000 | medium |
| 06 | equCab2 | 34 | 2,484,532,062 | 2,428,790,173 | 55,741,889 | % 40.97 | Horse | 6.8X | 91571448 | SyntenicNet | 56.504% | 3000 | medium |
| 07 | canFam2 | 41 | 2,531,673,953 | 2,384,996,543 | 146,677,410 | % 40.63 | Dog | 7.6X | 67211953 | SyntenicNet | 51.588% | 3000 | medium |
| 08 | mm9 | 35 | 2,725,765,481 | 2,620,345,972 | 105,419,509 | % 44.09 | Mouse | 20X | 131738871 | SyntenicNet | 32.044% | 3000 | medium |
| 09 | rn4 | 45 | 2,834,127,293 | 2,566,294,765 | 267,832,528 | % 44.29 | Rat | 20X | 143002779 | SyntenicNet | 30.350% | 3000 | medium |
| 10 | monDom5 | 11 | 3,605,631,728 | 3,501,660,299 | 103,971,429 | % 55.95 | Opossum | 6.8X | 527952102 | SyntenicNet | 13.743% | 5000 | loose |
| 11 | galGal3 | 57 | 1,100,480,441 | 1,042,583,135 | 57,897,306 | % 9.85 | Chicken | 6.6X | 94230402 | SyntenicNet | 4.557% | 5000 | loose |
| 12 | danRer7 | 1,133 | 1,412,464,843 | 1,409,770,109 | 2,694,734 | % 52.06 | Zebrafish | 30X | 54093808 | SyntenicNet | 2.558% | 5000 | loose |
