Ce11 26-way Genome size statistics: Difference between revisions

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(links to genome-preview instead of genome-test)
(add reference to pair-wise matrix)
 
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<LI>C. elegans 26-way [[Ce11 26-way conservation lastz parameters]]</LI>
<LI>C. elegans 26-way [[Ce11 26-way conservation lastz parameters]]</LI>
<LI>all other [[UCSC Multiple Alignments]]</LI>
<LI>all other [[UCSC Multiple Alignments]]</LI>
<LI>see also: [[Ws245ChainNet|matrix]] of all pair-wise alignments
</UL>
</UL>



Latest revision as of 18:10, 3 September 2015

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-preview 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-preview
chrom
count
total
size
non-N
bases
N base
count
% masked common name/
src info
coverage N50
chrom.sizes
alignment type % of ce11
matched
(chainLink table)
chain
minScore
chain
linearGap
01ce11 7 100,286,401100,286,401 0% 12.62 C. elegans30X 17493829 N/AN/A N/A N/A
02caeSp51 15,261 131,797,386130,391,159 1,406,227% 28.16 C. sp. 5 ju800  25228 Net40.332% 1000 loose
03caePb3 3,305 190,369,721170,093,638 20,276,083% 29.30 C. brenneri9.5X 381961 Net40.638% 1000 loose
04caeRem4 3,670 145,442,736138,406,203 7,036,533% 30.48 C. remanei9.2X 435512 Net41.715% 1000 loose
05cb4 13 108,434,085105,430,959 3,003,126% 36.52 C. briggsae10X 17485439 Net39.384% 1000 loose
06caeSp111 665 79,321,43376,497,192 2,824,241% 29.15 C. tropicalis20.2X 20921866 Net37.870% 1000 loose
07caeJap4 18,817 166,256,191154,057,934 12,198,257% 46.77 C. japonica22X 94149 Net27.709% 1000 loose
08caeAng2 34,621 105,997,62894,555,035 11,442,593% 39.91 C. angaria170X 79858 Net17.682% 1000 loose
09priPac3 18,084 172,510,819153,208,199 19,302,620% 23.93 P. pacificus  1244534 Net6.308% 1000 loose
10priExs1 4,369 177,536,987166,915,502 10,621,485% 23.30 P. exspectatus  142245 Net6.222% 1000 loose
11burXyl1 5,528 74,576,23973,100,506 1,475,733% 28.93 Pine wood nematode  949830 Net6.291% 1000 loose
12ancCey1 1,736 313,092,710300,901,610 12,191,100% 22.06 A. ceylanicum76.0X 668412 Net9.736% 1000 loose
13haeCon2 23,823 369,720,058345,915,897 23,804,161% 21.16 Barber pole worm  83299 Net8.936% 1000 loose
14necAme1 11,865 244,088,665208,187,215 35,901,450% 25.80 N. americanus26.15X 211861 Net8.902% 1000 loose
15panRed1 941 65,110,23662,090,108 3,020,128% 14.57 Microworm  262414 Net6.585% 1000 loose
16hetBac1 1,241 76,992,47774,374,900 2,617,577% 24.47 H. bacteriophora/m31e26.1X 312328 Net10.486% 1000 loose
17ascSuu1 12,989 269,573,965262,604,319 6,969,646% 21.48 Pig roundworm90X 413062 Net5.722% 1000 loose
18strRat2 135 43,150,24242,896,169 254,073% 55.64 Threadworm  11693564 Net5.669% 1000 loose
19triSpi1 6,864 63,542,12858,555,140 4,986,988% 33.95 Trichinella34.6X 6373445 Net2.848% 1000 loose
20triSui1 4,293 74,248,99571,825,189 2,423,806% 12.36 Whipworm140X 503034 Net2.917% 1000 loose
21melInc2 2,996 86,079,53482,112,681 3,966,853% 43.99 M. incognita  62516 Net3.516% 1000 loose
22melHap1 3,452 53,017,50753,017,507 0% 52.96 M. hapla10.4X 37608 Net3.916% 1000 loose
23bruMal2 9,781 95,156,66587,397,445 7,759,220% 38.02 Filarial worm  191089 Net5.065% 1000 loose
24oncVol1 710 97,402,14494,327,777 3,074,367% 37.03 O. volvulus  25485961 Net5.193% 1000 loose
25loaLoa1 5,765 91,379,42287,532,183 3,847,239% 32.15 Eye worm20X 174388 Net5.056% 1000 loose
26dirImm1 16,062 88,323,34384,892,734 3,430,609% 39.12 Dog heartworm  71281 Net5.005% 1000 loose