Hg19 Genome size statistics

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see also

statistics collected from UCSC 2bit files

  • The external links from the UCSC database name go to the sequencing center information pages for this 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 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
  • % masked == masked either with WindowMasker or RepeatMasker plus TRF simple repeats
  • % of hg19 matched (chainLink table) == featureBits hg19 chain<Db>Link == alignment coverage

do not edit, automatically generated table

order
count
ucsc
db name
chrom
count
total
size
non-N
bases
N base
count
% masked common name coverage N50
chrom.sizes
alignment type % of hg19
matched
(chainLink table)
chain
minScore
chain
linearGap
01hg19 93 3,137,161,2642,897,310,462 239,850,802% 50.63 Human20X 146364022 N/AN/A N/A N/A
02panTro2 52 3,350,447,5122,909,246,738 441,200,774% 48.90 Chimp6X 145085868 SyntenicNet94.846% 5000 medium
03gorGor1 609,861 2,323,645,8952,043,974,660 279,671,235% 47.27 Gorilla2X 11278 RecipBest59.484% 5000 medium
04ponAbe2 55 3,446,771,3963,093,543,172 353,228,224% 50.89 Orangutan6X 135191526 SyntenicNet91.350% 5000 medium
05rheMac2 22 2,864,106,0712,646,668,809 217,437,262% 48.28 Rhesus5.1X 153947521 SyntenicNet82.744% 5000 medium
06papHam1 387,374 2,867,564,6542,741,849,051 125,715,603% 48.70 Baboon5.3X 88525 RecipBest82.810% 5000 medium
07calJac1 49,724 3,029,401,8402,929,124,957 100,276,883% 47.50 Marmoset6X 303154 RecipBest70.860% 5000 medium
08tarSyr1 656,709 3,179,905,1322,768,536,343 411,368,789% 41.75 Tarsier2X 12214 RecipBest47.830% 3000 medium
09micMur1 185,042 2,902,270,7361,852,394,361 1,049,876,375% 37.31 Mouse lemur2X 140884 RecipBest46.519% 3000 medium
10otoGar1 120,882 3,420,058,8641,969,052,059 1,451,006,805% 34.89 Bushbaby2X 139426 RecipBest43.644% 3000 medium
11equCab2 34 2,484,532,0622,428,790,173 55,741,889% 40.97 Horse6.8X 91571448 SyntenicNet57.050% 3000 medium
12tupBel1 150,851 3,660,774,9572,137,225,476 1,523,549,481% 20.43 Tree shrew2X 127888 RecipBest36.156% 3000 medium
13turTru1 116,467 2,519,048,4862,298,444,090 220,604,396% 43.86 Dolphin2X 166056 RecipBest48.398% 3000 medium
14speTri1 160,889 3,488,768,5921,913,367,893 1,575,400,699% 26.90 Squirrel2X 97483 RecipBest35.713% 3000 medium
15vicPac1 298,413 2,962,253,6081,922,910,435 1,039,343,173% 32.24 Alpaca2X 230521 RecipBest39.399% 3000 medium
16choHof1 481,259 2,458,927,6202,060,419,685 398,507,935% 35.67 Sloth2X 9667 RecipBest34.377% 3000 medium
17pteVam1 96,944 1,996,076,4101,839,436,660 156,639,750% 31.75 Megabat2X 124060 RecipBest45.414% 3000 medium
18loxAfr3 2,353 3,196,760,8333,118,565,340 78,195,493% 47.63 Elephant7X 46401353 SyntenicNet46.636% 3000 medium
19felCat3 217,790 4,045,535,3221,642,698,377 2,402,836,945% 37.66 Cat2X 117081 RecipBest35.713% 3000 medium
20canFam2 41 2,531,673,9532,384,996,543 146,677,410% 40.63 Dog7.6X 67211953 SyntenicNet52.879% 3000 medium
21dasNov2 292,141 4,813,823,5622,371,493,872 2,442,329,690% 37.23 Armadillo2X 55360 RecipBest33.543% 3000 medium
22oryCun2 3,242 2,737,490,5012,604,023,284 133,467,217% 43.74 Rabbit6.51X 111795807 SyntenicNet44.317% 3000 medium
23myoLuc1 193,323 2,850,051,5591,673,855,868 1,176,195,691% 24.90 Microbat2X 97555 RecipBest33.174% 3000 medium
24bosTau4 11,900 2,917,974,5302,731,813,236 186,161,294% 46.89 Cow7.1X 85358539 SyntenicNet46.506% 3000 medium
25cavPor3 3,144 2,723,219,6412,663,369,733 59,849,908% 27.53 Guinea Pig6.76X 27942054 SyntenicNet43.680% 3000 medium
26proCap1 295,006 2,985,258,9992,407,847,681 577,411,318% 28.11 Rock hyrax2X 24297 RecipBest30.864% 3000 medium
27dipOrd1 210,053 2,158,502,0981,844,961,421 313,540,677% 28.28 Kangaroo rat2X 36427 RecipBest27.161% 3000 medium
28ochPri2 187,558 3,445,784,3541,923,624,051 1,522,160,303% 11.44 Pika2X 88760 RecipBest27.768% 3000 medium
29eriEur1 379,802 3,367,787,3582,133,134,836 1,234,652,522% 50.89 Hedgehog2X 33565 RecipBest19.362% 3000 medium
30echTel1 325,491 3,823,724,7282,111,581,369 1,712,143,359% 13.84 Tenrec2X 48377 RecipBest23.120% 3000 medium
31mm9 35 2,725,765,4812,620,345,972 105,419,509% 44.09 Mouse20X 131738871 SyntenicNet35.299% 3000 medium
32rn4 45 2,834,127,2932,566,294,765 267,832,528% 44.29 Rat20X 143002779 SyntenicNet32.879% 3000 medium
33sorAra1 262,057 2,936,119,0081,832,864,697 1,103,254,311% 39.07 Shrew2X 47941 RecipBest19.760% 3000 medium
34macEug1 616,418 2,944,879,1062,541,767,336 403,111,770% 36.24 Wallaby2X 16053 RecipBest6.011% 3000 medium
35monDom5 11 3,605,631,7283,501,660,299 103,971,429% 55.95 Opossum6.8X 527952102 SyntenicNet14.358% 5000 loose
36ornAna1 201,523 1,996,811,2121,842,235,522 154,575,690% 47.89 Platypus6X 991605 RecipBest7.627% 5000 loose
37galGal3 57 1,100,480,4411,042,583,135 57,897,306% 9.85 Chicken6.6X 94230402 SyntenicNet3.591% 5000 loose
38taeGut1 70 1,233,186,3411,222,864,691 10,321,650% 20.42 Zebra finch6X 73657157 SyntenicNet3.496% 5000 loose
39anoCar1 7,233 1,781,602,8991,741,478,929 40,123,970% 42.56 Lizard6.8X 2439125 SyntenicNet3.591% 5000 loose
40xenTro2 19,759 1,513,925,4921,359,400,017 154,525,475% 19.65 X. tropicalis7.65X 1564123 Net3.176% 5000 loose
41gasAcu1 23 463,354,448446,627,861 16,726,587% 2.58 Stickleback6X 20083130 Net1.916% 5000 loose
42fr2 2 400,525,790351,212,245 49,313,545% 19.01 Fugu8.5X 400509343 Net1.702% 5000 loose
43danRer6 11,724 1,512,402,3061,506,876,822 5,525,484% 51.69 Zebrafish6.5X 50748729 Net3.051% 5000 loose
44tetNig2 27 358,618,246302,314,788 56,303,458% 20.27 Tetraodon7.9X 13390619 Net1.712% 5000 loose
45oryLat2 7,189 869,000,216700,386,597 168,613,619% 33.09 Medaka10.6X 29908082 Net1.849% 5000 loose
46petMar1 108,241 1,027,258,967831,696,438 195,562,529% 40.67 Lamprey5.9X 14239 Net1.082% 5000 loose
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