DanRer7 Genome size statistics: Difference between revisions

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==see also==
==see also==
<UL>
<UL>
<LI>[[DanRer7 conservation alignment]]</LI>
<LI>Zebrafish 8-way [[DanRer7 conservation alignment]]</LI>
<LI>[[DanRer7 conservation lastz parameters]]</LI>
<LI>Zebrafish 8-way [[DanRer7 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>



Latest revision as of 20:18, 19 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 danRer7 matched (chainLink table) == featureBits danRer7 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 danRer7
matched
(chainLink table)
chain
minScore
chain
linearGap
01danRer7 1,133 1,412,464,8431,409,770,109 2,694,734% 52.06 Zebrafish30X 54093808 N/AN/A N/A N/A
02gasAcu1 23 463,354,448446,627,861 16,726,587% 2.58 Stickleback6X 20083130 MAF net10.270% 2000 medium
03oryLat2 7,189 869,000,216700,386,597 168,613,619% 33.09 Medaka10.6X 29908082 MAF net10.032% 2000 medium
04tetNig2 27 358,618,246302,314,788 56,303,458% 20.27 Tetraodon7.9X 13390619 MAF net6.273% 2000 medium
05fr2 2 400,525,790351,212,245 49,313,545% 19.01 Fugu8.5X 400509343 MAF net7.363% 2000 medium
06xenTro2 19,759 1,513,925,4921,359,400,017 154,525,475% 19.65 X. tropicalis7.65X 1564123 MAF net6.428% 5000 loose
07mm9 35 2,725,765,4812,620,345,972 105,419,509% 44.09 Mouse20X 131738871 MAF net5.104% 5000 loose
08hg19 93 3,137,161,2642,897,310,462 239,850,802% 50.63 Human20X 146364022 MAF net6.151% 5000 loose