Rn5 Genome size statistics

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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 rn5
matched
(chainLink table)
chain
minScore
chain
linearGap
01rn5 2,739 2,909,698,9382,572,853,723 336,845,215% 42.81 Rat6X 154597545 N/AN/A N/A N/A
02mm10 66 2,730,871,7742,652,783,500 78,088,274% 45.18 Mouse20X 130694993 Net70.278% 5000 medium
03cavPor3 3,144 2,723,219,6412,663,369,733 59,849,908% 27.53 Guinea pig6.76X 27942054 Net29.127% 3000 medium
04hg19 93 3,137,161,2642,897,310,462 239,850,802% 50.63 Human20X 146364022 Net36.299% 3000 medium
05panTro4 24,129 3,309,577,9222,902,338,967 407,238,955% 51.29 Chimp6X 143986469 Net35.616% 3000 medium
06rheMac3 34,103 2,969,988,1802,639,145,830 330,842,350% 48.54 Rhesus50X 150158102 Net34.835% 3000 medium
07canFam3 3,268 2,410,976,8752,392,715,236 18,261,639% 43.01 Dog7.6X 63241923 Net29.852% 3000 medium
08ailMel1 81,467 2,299,509,0152,245,312,831 54,196,184% 38.96 Panda73X 1281781 Net31.818% 1000 N/A
09bosTau7 11,692 2,981,119,5792,804,673,174 176,446,405% 49.56 Cow7.1X 85119472 Net26.820% 3000 medium
10monDom5 11 3,605,631,7283,501,660,299 103,971,429% 55.95 Opossum6.8X 527952102 Net9.694% 5000 loose
11galGal4 15,932 1,046,932,0991,032,854,810 14,077,289% 20.41 Chicken12X 90216835 Net3.788% 5000 loose
12melGal1 5,891 1,061,817,101935,922,386 125,894,715% 6.60 Turkey5X 74864452 Net3.630% 5000 loose
13danRer7 1,133 1,412,464,8431,409,770,109 2,694,734% 52.06 Zebrafish30X 54093808 Net2.588% 5000 loose