Marmoset calJac3 13-way size statistics: Difference between revisions

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<UL>
<UL>
<LI>[[Hg19 Genome size statistics]]</LI>
<LI>Marmoset 13-way [[CalJac3 conservation alignment]]</LI>
<LI>[[Hg19 conservation alignment]]</LI>
<LI>Marmoset 13-way [[CalJac3 conservation lastz parameters]]</LI>
<LI>[[Hg19 conservation lastz parameters]]</LI>
<LI>all other [[UCSC Multiple Alignments]]</LI>
<LI>[[Hg18 44way alignment]]</LI>
<LI>[[Hg18 44way blastz parameters]]</LI>
<LI>[[Genome size statistics|Hg18 genome size statistics]]</LI>
</UL>
</UL>


Latest revision as of 22:49, 18 May 2011

see also

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 calJac3 matched (chainLink table) == featureBits calJac3 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 calJac3
matched
(chainLink table)		 chain
minScore		 chain
linearGap
01 calJac3 14,205 2,914,958,5442,752,505,800 162,452,744% 47.71 Marmoset6X 132174527 N/AN/A N/AN/A
02 ponAbe2 55 3,446,771,3963,093,543,172 353,228,224% 50.89 Orangutan6X 135191526 SyntenicNet71.893% 5000medium
03 hg19 93 3,137,161,2642,897,310,462 239,850,802% 50.63 Human20X 146364022 SyntenicNet73.768% 5000medium
04 panTro2 52 3,350,447,5122,909,246,738 441,200,774% 48.90 Chimp6X 145085868 SyntenicNet72.304% 5000medium
05 gorGor2 58,049 3,035,791,6222,829,687,208 206,104,414% 48.19 Gorilla2X 913458 RecipBest76.343% 3000medium
06 rheMac2 22 2,864,106,0712,646,668,809 217,437,262% 48.28 Rhesus5.1X 153947521 SyntenicNet69.625% 5000medium
07 papHam1 387,374 2,867,564,6542,741,849,051 125,715,603% 48.70 Baboon5.3X 88525 RecipBest70.053% 5000medium
08 tarSyr1 656,709 3,179,905,1322,768,536,343 411,368,789% 41.75 Tarsier2X 12214 RecipBest46.729% 3000medium
09 micMur1 185,042 2,902,270,7361,852,394,361 1,049,876,375% 37.31 Mouse lemur2X 140884 RecipBest45.726% 3000medium
10 otoGar1 120,882 3,420,058,8641,969,052,059 1,451,006,805% 34.89 Bushbaby2X 139426 RecipBest42.743% 3000medium
11 mm9 35 2,725,765,4812,620,345,972 105,419,509% 44.09 Mouse20X 131738871 SyntenicNet31.310% 3000medium
12 canFam2 41 2,531,673,9532,384,996,543 146,677,410% 40.63 Dog7.6X 67211953 SyntenicNet50.766% 3000medium
13 monDom5 11 3,605,631,7283,501,660,299 103,971,429% 55.95 Opossum6.8X 527952102 SyntenicNet7.906% 5000loose
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