TarSyr2 17-way Genome size statistics

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Revision as of 04:56, 20 December 2014 by Hiram (talk | contribs) (updated order after 4D calculation)
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see also

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
01tarSyr2 337,189 3,453,864,7743,405,755,564 48,109,210% 47.85 Tarsier48X 401181 N/AN/A N/A N/A
02panPan1 10,867 2,869,190,0712,725,905,606 143,284,465% 36.53 Bonobo26X 10124892 RecipBest52.289% 3000 medium
03panTro4 24,129 3,309,577,9222,902,338,967 407,238,955% 51.29 Chimp6X 143986469 SyntenicNet51.284% 3000 medium
04ponAbe2 55 3,446,771,3963,093,543,172 353,228,224% 50.89 Orangutan6X 135191526 SyntenicNet51.302% 3000 medium
05gorGor3 46,823 3,029,553,6462,822,760,080 206,793,566% 48.80 Gorilla2.1X 145327772 RecipBest50.262% 3000 medium
06nomLeu3 17,492 2,962,077,4492,756,609,047 205,468,402% 51.14 Gibbon5.6X 117381234 SyntenicNet50.545% 3000 medium
07macFas5 7,601 2,946,843,7372,803,866,385 142,977,352% 50.11 Crab-eating macaque68X 152835861 SyntenicNet51.814% 3000 medium
08papAnu2 63,250 2,948,380,7102,893,250,291 55,130,419% 38.95 Baboon85X 139646187 SyntenicNet51.652% 3000 medium
09rheMac3 34,103 2,969,988,1802,639,145,830 330,842,350% 48.54 Rhesus50X 150158102 SyntenicNet50.710% 3000 medium
10chlSab2 2,004 2,789,656,3282,752,000,999 37,655,329% 48.77 Green monkey95X 101219884 SyntenicNet51.691% 3000 medium
11hg38 455 3,209,286,1053,049,315,783 159,970,322% 52.10 Human20X 145138636 SyntenicNet52.305% 3000 medium
12rhiRox1 319,549 3,011,966,1702,397,093,190 614,872,980% 46.33 Golden snub-nosed monkey53.7X 137426304 RecipBest47.155% 3000 medium
13nasLar1 319,550 3,011,982,7402,397,109,760 614,872,980% 46.33 Proboscis monkey290X 137426304 RecipBest47.164% 3000 medium
14saiBol1 2,685 2,608,572,0642,477,131,095 131,440,969% 46.69 Squirrel monkey80X 18744880 RecipBest48.208% 3000 medium
15micMur1 185,042 2,902,270,7361,852,394,361 1,049,876,375% 37.31 Mouse lemur2X 140884 RecipBest38.087% 3000 medium
16calJac3 14,205 2,914,958,5442,752,505,800 162,452,744% 47.71 Marmoset6X 132174527 SyntenicNet48.629% 3000 medium
17otoGar3 7,793 2,519,724,5502,359,530,453 160,194,097% 39.51 Bushbaby137X 13852661 RecipBest44.814% 3000 medium