DanRer10 12-way 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-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 danRer10
matched
(chainLink table)
chain
minScore
chain
linearGap
01danRer10 1,061 1,371,719,3831,369,631,918 2,087,465% 52.32 Zebrafish30X 53345113 N/AN/A N/A N/A
02gasAcu1 23 463,354,448446,627,861 16,726,587% 2.58 Stickleback6X 20083130 Net9.814% 2000 medium
03lepOcu1 1,925 945,874,548869,414,359 76,460,189% 24.85 Spotted gar677.5X 50348508 Net8.409% 5000 loose
04tetNig2 27 358,618,246302,314,788 56,303,458% 20.27 Tetraodon7.9X 13390619 Net6.063% 2000 medium
05fr3 6,835 391,484,715350,961,831 40,522,884% 19.01 Fugu8.5X 11516971 Net7.080% 2000 medium
06oryLat2 7,189 869,000,216700,386,597 168,613,619% 33.09 Medaka10.6X 29908082 Net9.640% 2000 medium
07xenTro9 6,822 1,440,398,4541,369,865,365 70,533,089% 34.42 X. tropicalis7.6X 135134832 Net6.731% 5000 loose
08galGal6 464 1,065,365,4251,055,580,959 9,784,466% 21.41 Chicken82X 91315245 Net5.871% 1000 loose
09calMil1 21,204 974,498,586936,953,443 37,545,143% 28.08 Elephant shark19.25X 4521921 Net5.599% 5000 loose
10hg38 640 3,272,116,9503,110,748,256 161,368,694% 52.11 Human20X 145138636 Net7.110% 5000 loose
11mm10 66 2,730,871,7742,652,783,500 78,088,274% 45.18 Mouse20X 130694993 Net5.228% 5000 loose
12latCha1 22,819 2,860,591,9212,183,592,768 676,999,153% 45.68 Coelacanth77.5X 924513 Net6.319% 5000 loose