PanTro3 Genome size statistics: Difference between revisions

From genomewiki
Jump to navigationJump to search
(other panTro3 link)
(fixup links to others)
 
Line 1: Line 1:
==see also==
<UL>
<UL>
<LI>[[PanTro3 conservation lastz parameters]]</LI>
<LI>Chimp 12-way [[PanTro3 conservation alignment]]</LI>
<LI>[[PanTro3 conservation alignment]]</LI>
<LI>Chimp 12-way [[PanTro3 conservation lastz parameters]]</LI>
<LI>[[Hg19 conservation alignment]]</LI>
<LI>all other [[UCSC Multiple Alignments]]</LI>
<LI>[[Hg19 conservation lastz parameters]]</LI>
<LI>[[Hg18 44way alignment]]</LI>
<LI>[[Hg18 44way blastz parameters]]</LI>
<LI>[[Genome size statistics|Hg18 genome size statistics]]</LI>
<LI>[[Marmoset calJac3 13-way size statistics]]</LI>
</UL>
</UL>


Line 19: Line 16:
<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 hg19 matched (chainLink table) == featureBits hg19 chain<Db>Link == alignment coverage</LI>
<LI>% of panTro3 matched (chainLink table) == featureBits panTro3 chain<Db>Link == alignment coverage</LI>
</UL>
</UL>


Latest revision as of 22:37, 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 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
01panTro3 24,132 3,307,960,4322,900,529,764 407,430,668% 50.64 Chimp6X 143986469 N/AN/A 1000 N/A
02hg19 93 3,137,161,2642,897,310,462 239,850,802% 50.63 Human20X 146364022 SynetnicNet95.597% 5000 medium
03ponAbe2 55 3,446,771,3963,093,543,172 353,228,224% 50.89 Orangutan6X 135191526 SyntenicNet89.586% 5000 medium
04rheMac2 22 2,864,106,0712,646,668,809 217,437,262% 48.28 Rhesus5.1X 153947521 SyntenicNet81.342% 5000 medium
05calJac3 14,205 2,914,958,5442,752,505,800 162,452,744% 47.71 Marmoset6X 132174527 SyntenicNet69.662% 5000 medium
06equCab2 34 2,484,532,0622,428,790,173 55,741,889% 40.97 Horse6.8X 91571448 SyntenicNet56.504% 3000 medium
07canFam2 41 2,531,673,9532,384,996,543 146,677,410% 40.63 Dog7.6X 67211953 SyntenicNet51.588% 3000 medium
08mm9 35 2,725,765,4812,620,345,972 105,419,509% 44.09 Mouse20X 131738871 SyntenicNet32.044% 3000 medium
09rn4 45 2,834,127,2932,566,294,765 267,832,528% 44.29 Rat20X 143002779 SyntenicNet30.350% 3000 medium
10monDom5 11 3,605,631,7283,501,660,299 103,971,429% 55.95 Opossum6.8X 527952102 SyntenicNet13.743% 5000 loose
11galGal3 57 1,100,480,4411,042,583,135 57,897,306% 9.85 Chicken6.6X 94230402 SyntenicNet4.557% 5000 loose
12danRer7 1,133 1,412,464,8431,409,770,109 2,694,734% 52.06 Zebrafish30X 54093808 SyntenicNet2.558% 5000 loose
Retrieved from "https://genomewiki.ucsc.edu/index.php?title=PanTro3_Genome_size_statistics&oldid=14027"