PetMar2 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 petMar2
matched
(chainLink table)
chain
minScore
chain
linearGap
01petMar2 25,006 885,550,958647,368,134 238,182,824% 42.47 Lamprey5.0X 184619 N/AN/A N/A N/A
02galGal4 15,932 1,046,932,0991,032,854,810 14,077,289% 20.41 Chicken12X 90216835 Net2.869% 5000 loose
03oryLat2 7,189 869,000,216700,386,597 168,613,619% 33.09 Medaka10.6X 29908082 Net4.926% 5000 loose
04monDom5 11 3,605,631,7283,501,660,299 103,971,429% 55.95 Opossum6.8X 527952102 Net2.618% 5000 loose
05hg19 93 3,137,161,2642,897,310,462 239,850,802% 50.63 Human20X 146364022 Net3.324% 5000 loose
06mm10 66 2,730,871,7742,652,783,500 78,088,274% 45.18 Mouse20X 130694993 Net3.232% 5000 loose
07braFlo2 399 521,910,208480,418,582 41,491,626% 25.49 Lancelet11.5X 2586727 Net3.020% 5000 loose