Rn6 20-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 rn6
matched
(chainLink table)
chain
minScore
chain
linearGap
01rn6 953 2,870,182,9092,729,860,805 140,322,104% 43.31 Rat10X 145729302 N/AN/A N/A N/A
02mm10 66 2,730,871,7742,652,783,500 78,088,274% 45.18 Mouse20X 130694993 SyntenicNet71.015% 5000 medium
03micOch1 6,335 2,287,340,9432,104,321,675 183,019,268% 23.89 Prairie vole94X 61813736 SyntenicNet57.205% 3000 medium
04cavPor3 3,144 2,723,219,6412,663,369,733 59,849,908% 27.53 Guinea pig6.76X 27942054 SyntenicNet27.834% 3000 medium
05hg38 455 3,209,286,1053,049,315,783 159,970,322% 52.10 Human20X 145138636 SyntenicNet34.899% 3000 medium
06panTro5 44,449 3,231,170,6663,132,619,616 98,551,050% 52.72 Chimp6X 135926727 SyntenicNet40.816% 3000 medium
07tarSyr2 337,189 3,453,864,7743,405,755,564 48,109,210% 47.85 Tarsier48X 401181 RecipBest38.509% 3000 medium
08rheMac8 284,728 3,236,224,3323,142,091,753 94,132,579% 54.33 Rhesus47.4X 144306982 SyntenicNet40.165% 3000 medium
09canFam3 3,268 2,410,976,8752,392,715,236 18,261,639% 43.01 Dog7.6X 63241923 SyntenicNet28.540% 3000 medium
10oryCun2 3,242 2,737,490,5012,604,023,284 133,467,217% 43.74 Rabbit6.51X 111795807 SyntenicNet24.654% 3000 medium
11felCat8 267,625 2,641,342,2582,599,700,169 41,642,089% 44.41 Cat20X 142431058 SyntenicNet29.520% 3000 medium
12ailMel1 81,467 2,299,509,0152,245,312,831 54,196,184% 38.96 Panda73X 1281781 RecipBest30.404% 3000 medium
13bosTau8 3,179 2,670,044,5002,649,304,231 20,740,269% 48.69 Cow9X 105708250 SyntenicNet25.902% 3000 medium
14monDom5 11 3,605,631,7283,501,660,299 103,971,429% 55.95 Opossum6.8X 527952102 SyntenicNet9.652% 5000 loose
15ornAna2 201,525 1,996,826,5131,842,250,823 154,575,690% 48.56 Platypus6X 991605 Net6.389% 5000 loose
16xenTro7 7,728 1,437,530,8791,365,936,747 71,594,132% 33.98 X. tropicalis7.44X 124127367 Net4.104% 5000 loose
17galGal5 23,475 1,230,258,5571,218,492,533 11,766,024% 25.74 Chicken70X 82310166 Net3.983% 5000 loose
18melGal5 231,286 1,128,339,1361,093,044,709 35,294,427% 22.09 Turkey35X 59006440 Net2.440% 5000 loose
19calMil1 21,204 974,498,586936,953,443 37,545,143% 28.08 Elephant shark19.25X 4521921 Net1.664% 5000 loose
20danRer10 1,061 1,371,719,3831,369,631,918 2,087,465% 52.32 Zebrafish30X 53345113 Net3.232% 5000 loose