Mm39 35-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 mm39
matched
(chainLink table)
chain
minScore
chain
linearGap
01mm39 61 2,728,222,4512,654,621,783 73,600,668% 45.00 Mouse20X 130530862 N/AN/A N/A N/A
02rn6 953 2,870,182,9092,729,860,805 140,322,104% 43.31 Rat10X 145729302 SyntenicNet70.901% 5000 medium
03GCF_003668045.3 647 2,366,634,3742,364,208,470 2,425,904% 31.58 Cricetulus griseus31X 1294537483 SyntenicNet58.000% 3000 medium
04casCan1 21,157 2,518,306,5652,517,974,654 331,911% 32.86 Beaver110X 317708 RecipBest36.600% 3000 medium
05speTri2 12,483 2,478,393,7702,311,060,300 167,333,470% 36.27 Squirrel495X 8192786 RecipBest34.147% 3000 medium
06manPen1 92,770 2,204,741,2411,998,946,804 205,794,437% 32.83 Chinese pangolin61X 117920 RecipBest27.322% 3000 medium
07cavPor3 3,144 2,723,219,6412,663,369,733 59,849,908% 27.53 Guinea pig6.76X 27942054 SyntenicNet28.378% 3000 medium
08galVar1 179,514 3,187,660,5722,802,837,430 384,823,142% 38.66 Malayan flying lemur55X 245189 Net35.714% 3000 medium
09calJac4 964 2,897,824,4272,859,816,984 38,007,443% 49.16 Marmoset40X 137671225 SyntenicNet33.090% 3000 medium
10gorGor6 5,486 3,044,872,2142,999,027,915 45,844,299% 50.29 Gorilla66.9X 127988552 SyntenicNet35.064% 3000 medium
11hg38 640 3,272,116,9503,110,748,256 161,368,694% 52.11 Human20X 145138636 SyntenicNet35.372% 3000 medium
12panPan3 4,293 3,051,901,3373,015,350,297 36,551,040% 50.21 Bonobo74X 129867894 SyntenicNet35.282% 3000 medium
13panTro6 4,346 3,050,398,0823,018,592,990 31,805,092% 53.55 Chimp124X 130782606 SyntenicNet35.291% 3000 medium
14tarSyr2 337,189 3,453,864,7743,405,755,564 48,109,210% 47.85 Tarsier48X 401181 RecipBest32.278% 3000 medium
15rheMac10 2,939 2,971,331,5302,936,892,725 34,438,805% 52.41 Rhesus50X 145679320 SyntenicNet34.838% 3000 medium
16otoGar3 7,793 2,519,724,5502,359,530,453 160,194,097% 39.51 Bushbaby137X 13852661 RecipBest29.729% 3000 medium
17equCab3 4,701 2,506,966,1352,497,530,654 9,435,481% 44.49 Horse88X 87230776 SyntenicNet34.831% 3000 medium
18turTru2 240,901 2,551,996,5732,332,402,443 219,594,130% 43.56 Dolphin3.5X 116261 RecipBest30.188% 3000 medium
19canFam4 2,198 2,482,000,0802,481,941,580 58,500% 43.54 Dog100X 64299765 SyntenicNet29.376% 3000 medium
20tupBel1 150,851 3,660,774,9572,137,225,476 1,523,549,481% 20.43 Tree shrew2X 127888 RecipBest19.691% 3000 medium
21susScr3 4,583 2,808,525,9912,518,987,191 289,538,800% 44.30 Pig24X 148491826 RecipBest25.611% 3000 medium
22loxAfr3 2,353 3,196,760,8333,118,565,340 78,195,493% 47.63 Elephant7X 46401353 RecipBest25.756% 3000 medium
23oryCun2 3,242 2,737,490,5012,604,023,284 133,467,217% 43.74 Rabbit6.51X 111795807 RecipBest25.182% 3000 medium
24oviAri4 5,466 2,615,516,2992,587,507,373 28,008,926% 45.81 Sheep166X 100009711 SyntenicNet26.200% 3000 medium
25neoSch1 7,872 2,400,839,3082,347,122,535 53,716,773% 43.31 Hawaiian monk seal61X 29518589 SyntenicNet31.257% 3000 medium
26bosTau9 2,211 2,715,853,7922,715,825,630 28,162% 49.35 Cow80X 103308737 RecipBest26.588% 3000 medium
27ochPri3 10,420 2,229,835,7161,943,987,870 285,847,846% 29.53 Pika103X 26863993 RecipBest18.559% 3000 medium
28eriEur2 5,803 2,715,720,9252,333,073,535 382,647,390% 45.60 Hedgehog79X 3264618 RecipBest13.450% 3000 medium
29echTel2 8,402 2,947,024,2862,605,196,361 341,827,925% 28.26 Tenrec78X 45764842 RecipBest14.456% 3000 medium
30sorAra2 12,845 2,423,158,1832,192,103,426 231,054,757% 32.76 Shrew120X 22794405 RecipBest13.370% 3000 medium
31monDom5 11 3,605,631,7283,501,660,299 103,971,429% 55.95 Opossum6.8X 527952102 Net5.382% 5000 loose
32xenTro9 6,822 1,440,398,4541,369,865,365 70,533,089% 34.42 X. tropicalis7.6X 135134832 Net1.936% 5000 loose
33galGal6 464 1,065,365,4251,055,580,959 9,784,466% 21.41 Chicken82X 91315245 Net2.537% 5000 loose
34petMar3 12,062 1,130,433,8971,043,181,598 87,252,299% 45.11 Lamprey100X 11932523 Net0.905% 5000 loose
35danRer11 1,923 1,679,203,4691,674,509,851 4,693,618% 51.76 Zebrafish30X 52186027 Net1.416% 5000 loose