TarSyr2 17-way Genome size statistics: Difference between revisions
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<TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AGCE01 Squirrel monkey]</TD><TH ALIGN=CENTER>80X</TH> | <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AGCE01 Squirrel monkey]</TD><TH ALIGN=CENTER>80X</TH> | ||
<TH ALIGN=CENTER>18744880</TH> | <TH ALIGN=CENTER>18744880</TH> | ||
<TH ALIGN=CENTER> | <TH ALIGN=CENTER>RecipBest</TH><TD ALIGN=RIGHT>48.208%</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>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AJFE01 Bonobo]</TD><TH ALIGN=CENTER>26X</TH> | <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AJFE01 Bonobo]</TD><TH ALIGN=CENTER>26X</TH> | ||
<TH ALIGN=CENTER>10124892</TH> | <TH ALIGN=CENTER>10124892</TH> | ||
<TH ALIGN=CENTER> | <TH ALIGN=CENTER>RecipBest</TH><TD ALIGN=RIGHT>52.289%</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>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=CABD02 Gorilla]</TD><TH ALIGN=CENTER>2.1X</TH> | <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=CABD02 Gorilla]</TD><TH ALIGN=CENTER>2.1X</TH> | ||
<TH ALIGN=CENTER>145327772</TH> | <TH ALIGN=CENTER>145327772</TH> | ||
<TD ALIGN=CENTER> | <TD ALIGN=CENTER>RecipBest</TD><TD ALIGN=RIGHT>50.262%</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>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=JMHX01 Proboscis monkey]</TD><TH ALIGN=CENTER>290X</TH> | <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=JMHX01 Proboscis monkey]</TD><TH ALIGN=CENTER>290X</TH> | ||
<TH ALIGN=CENTER>137426304</TH> | <TH ALIGN=CENTER>137426304</TH> | ||
<TH ALIGN=CENTER> | <TH ALIGN=CENTER>RecipBest</TH><TD ALIGN=RIGHT>47.164%</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>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=JABR01 Golden snub-nosed monkey]</TD><TH ALIGN=CENTER>53.7X</TH> | <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=JABR01 Golden snub-nosed monkey]</TD><TH ALIGN=CENTER>53.7X</TH> | ||
<TH ALIGN=CENTER>137426304</TH> | <TH ALIGN=CENTER>137426304</TH> | ||
<TH ALIGN=CENTER> | <TH ALIGN=CENTER>RecipBest</TH><TD ALIGN=RIGHT>47.155%</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>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ABDC00 Mouse lemur]</TD><TH ALIGN=CENTER>2X</TH> | <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ABDC00 Mouse lemur]</TD><TH ALIGN=CENTER>2X</TH> | ||
<TH ALIGN=CENTER>140884</TH> | <TH ALIGN=CENTER>140884</TH> | ||
<TD ALIGN=CENTER> | <TD ALIGN=CENTER>RecipBest</TD><TD ALIGN=RIGHT>38.087%</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>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AAQR03 Bushbaby]</TD><TH ALIGN=CENTER>137X</TH> | <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AAQR03 Bushbaby]</TD><TH ALIGN=CENTER>137X</TH> | ||
<TH ALIGN=CENTER>13852661</TH> | <TH ALIGN=CENTER>13852661</TH> | ||
<TH ALIGN=CENTER> | <TH ALIGN=CENTER>RecipBest</TH><TD ALIGN=RIGHT>44.814%</TD> | ||
<TD ALIGN=RIGHT>3000</TD> | <TD ALIGN=RIGHT>3000</TD> | ||
<TD ALIGN=CENTER>medium</TD></TR> | <TD ALIGN=CENTER>medium</TD></TR> | ||
</TABLE> | </TABLE> | ||
Revision as of 19:47, 19 December 2014
see also
- Tarsier 17-way TarSyr2 17-way conservation alignment
- Tarsier 17-way TarSyr2 17-way conservation lastz parameters
- all other UCSC Multiple Alignments
statistics collected from UCSC 2bit files
- The external link in the first column goes to the FTP location where the genome sequence was obtained
- The external links from the UCSC database name go to the UCSC genome-test browser for that 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 % masked is masking from Repeat Masker or Window Masker plus TRF/Simple Repeats, whichever is greater, usually WindowMasker for these genomes
- The common name external links go to information pages for this genome
- 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
do not edit, automatically generated table
| order count/ ftp src |
ucsc db name/ genome-test |
chrom count |
total size |
non-N bases |
N base count |
% masked | common name/ src info |
coverage | N50 chrom.sizes |
alignment type | % of tarSyr2 matched (chainLink table) |
chain minScore |
chain linearGap |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 01 | tarSyr2 | 337,189 | 3,453,864,774 | 3,405,755,564 | 48,109,210 | % 47.85 | Tarsier | 48X | 401181 | N/A | N/A | N/A | N/A |
| 02 | saiBol1 | 2,685 | 2,608,572,064 | 2,477,131,095 | 131,440,969 | % 46.69 | Squirrel monkey | 80X | 18744880 | RecipBest | 48.208% | 3000 | medium |
| 03 | hg38 | 455 | 3,209,286,105 | 3,049,315,783 | 159,970,322 | % 52.10 | Human | 20X | 145138636 | SyntenicNet | 52.305% | 3000 | medium |
| 04 | panPan1 | 10,867 | 2,869,190,071 | 2,725,905,606 | 143,284,465 | % 36.53 | Bonobo | 26X | 10124892 | RecipBest | 52.289% | 3000 | medium |
| 05 | gorGor3 | 46,823 | 3,029,553,646 | 2,822,760,080 | 206,793,566 | % 48.80 | Gorilla | 2.1X | 145327772 | RecipBest | 50.262% | 3000 | medium |
| 06 | panTro4 | 24,129 | 3,309,577,922 | 2,902,338,967 | 407,238,955 | % 51.29 | Chimp | 6X | 143986469 | SyntenicNet | 51.284% | 3000 | medium |
| 07 | nomLeu3 | 17,492 | 2,962,077,449 | 2,756,609,047 | 205,468,402 | % 51.14 | Gibbon | 5.6X | 117381234 | SyntenicNet | 50.545% | 3000 | medium |
| 08 | ponAbe2 | 55 | 3,446,771,396 | 3,093,543,172 | 353,228,224 | % 50.89 | Orangutan | 6X | 135191526 | SyntenicNet | 51.302% | 3000 | medium |
| 09 | nasLar1 | 319,550 | 3,011,982,740 | 2,397,109,760 | 614,872,980 | % 46.33 | Proboscis monkey | 290X | 137426304 | RecipBest | 47.164% | 3000 | medium |
| 10 | rhiRox1 | 319,549 | 3,011,966,170 | 2,397,093,190 | 614,872,980 | % 46.33 | Golden snub-nosed monkey | 53.7X | 137426304 | RecipBest | 47.155% | 3000 | medium |
| 11 | chlSab2 | 2,004 | 2,789,656,328 | 2,752,000,999 | 37,655,329 | % 48.77 | Green monkey | 95X | 101219884 | SyntenicNet | 51.691% | 3000 | medium |
| 12 | macFas5 | 7,601 | 2,946,843,737 | 2,803,866,385 | 142,977,352 | % 50.11 | Crab-eating macaque | 68X | 152835861 | SyntenicNet | 51.814% | 3000 | medium |
| 13 | rheMac3 | 34,103 | 2,969,988,180 | 2,639,145,830 | 330,842,350 | % 48.54 | Rhesus | 50X | 150158102 | SyntenicNet | 50.710% | 3000 | medium |
| 14 | papAnu2 | 63,250 | 2,948,380,710 | 2,893,250,291 | 55,130,419 | % 38.95 | Baboon | 85X | 139646187 | SyntenicNet | 51.652% | 3000 | medium |
| 15 | calJac3 | 14,205 | 2,914,958,544 | 2,752,505,800 | 162,452,744 | % 47.71 | Marmoset | 6X | 132174527 | SyntenicNet | 48.629% | 3000 | medium |
| 16 | micMur1 | 185,042 | 2,902,270,736 | 1,852,394,361 | 1,049,876,375 | % 37.31 | Mouse lemur | 2X | 140884 | RecipBest | 38.087% | 3000 | medium |
| 17 | otoGar3 | 7,793 | 2,519,724,550 | 2,359,530,453 | 160,194,097 | % 39.51 | Bushbaby | 137X | 13852661 | RecipBest | 44.814% | 3000 | medium |
